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- PDB-9z9c: Crystal structure of a glyceraldehyde-3-phosphate dehydrogenase f... -

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Basic information

Entry
Database: PDB / ID: 9z9c
TitleCrystal structure of a glyceraldehyde-3-phosphate dehydrogenase from Neisseria gonorrhoeae in complex with NAD (P1 form)
ComponentsGlyceraldehyde-3-phosphate dehydrogenase
KeywordsOXIDOREDUCTASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE
Function / homology
Function and homology information


Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor / oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor / glucose metabolic process / NAD binding / NADP binding
Similarity search - Function
Glyceraldehyde 3-phosphate dehydrogenase, active site / Glyceraldehyde 3-phosphate dehydrogenase active site. / Glyceraldehyde-3-phosphate dehydrogenase, type I / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD(P) binding domain / Glyceraldehyde 3-phosphate dehydrogenase, catalytic domain / Glyceraldehyde/Erythrose phosphate dehydrogenase family / Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / TRIETHYLENE GLYCOL / Glyceraldehyde-3-phosphate dehydrogenase
Similarity search - Component
Biological speciesNeisseria gonorrhoeae NCCP11945 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00036 United States
National Institutes of Health/Office of the DirectorS10OD030394 United States
CitationJournal: To be published
Title: Crystal structure of a glyceraldehyde-3-phosphate dehydrogenase from Neisseria gonorrhoeae in complex with NAD (P1 form)
Authors: Liu, L. / Lovell, S. / Seibold, S. / Battaile, K.P.
History
DepositionNov 18, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glyceraldehyde-3-phosphate dehydrogenase
B: Glyceraldehyde-3-phosphate dehydrogenase
C: Glyceraldehyde-3-phosphate dehydrogenase
D: Glyceraldehyde-3-phosphate dehydrogenase
E: Glyceraldehyde-3-phosphate dehydrogenase
F: Glyceraldehyde-3-phosphate dehydrogenase
G: Glyceraldehyde-3-phosphate dehydrogenase
H: Glyceraldehyde-3-phosphate dehydrogenase
I: Glyceraldehyde-3-phosphate dehydrogenase
J: Glyceraldehyde-3-phosphate dehydrogenase
K: Glyceraldehyde-3-phosphate dehydrogenase
L: Glyceraldehyde-3-phosphate dehydrogenase
M: Glyceraldehyde-3-phosphate dehydrogenase
N: Glyceraldehyde-3-phosphate dehydrogenase
O: Glyceraldehyde-3-phosphate dehydrogenase
P: Glyceraldehyde-3-phosphate dehydrogenase
Q: Glyceraldehyde-3-phosphate dehydrogenase
R: Glyceraldehyde-3-phosphate dehydrogenase
S: Glyceraldehyde-3-phosphate dehydrogenase
T: Glyceraldehyde-3-phosphate dehydrogenase
U: Glyceraldehyde-3-phosphate dehydrogenase
V: Glyceraldehyde-3-phosphate dehydrogenase
W: Glyceraldehyde-3-phosphate dehydrogenase
X: Glyceraldehyde-3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)899,98749
Polymers883,91524
Non-polymers16,07225
Water13,619756
1
A: Glyceraldehyde-3-phosphate dehydrogenase
B: Glyceraldehyde-3-phosphate dehydrogenase
C: Glyceraldehyde-3-phosphate dehydrogenase
D: Glyceraldehyde-3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,9738
Polymers147,3194
Non-polymers2,6544
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19670 Å2
ΔGint-121 kcal/mol
Surface area42710 Å2
MethodPISA
2
E: Glyceraldehyde-3-phosphate dehydrogenase
F: Glyceraldehyde-3-phosphate dehydrogenase
G: Glyceraldehyde-3-phosphate dehydrogenase
H: Glyceraldehyde-3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,1239
Polymers147,3194
Non-polymers2,8045
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19390 Å2
ΔGint-119 kcal/mol
Surface area43160 Å2
MethodPISA
3
I: Glyceraldehyde-3-phosphate dehydrogenase
J: Glyceraldehyde-3-phosphate dehydrogenase
K: Glyceraldehyde-3-phosphate dehydrogenase
L: Glyceraldehyde-3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,9738
Polymers147,3194
Non-polymers2,6544
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19660 Å2
ΔGint-124 kcal/mol
Surface area43020 Å2
MethodPISA
4
M: Glyceraldehyde-3-phosphate dehydrogenase
N: Glyceraldehyde-3-phosphate dehydrogenase
O: Glyceraldehyde-3-phosphate dehydrogenase
P: Glyceraldehyde-3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,9738
Polymers147,3194
Non-polymers2,6544
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19620 Å2
ΔGint-113 kcal/mol
Surface area43100 Å2
MethodPISA
5
Q: Glyceraldehyde-3-phosphate dehydrogenase
R: Glyceraldehyde-3-phosphate dehydrogenase
S: Glyceraldehyde-3-phosphate dehydrogenase
T: Glyceraldehyde-3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,9738
Polymers147,3194
Non-polymers2,6544
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19560 Å2
ΔGint-118 kcal/mol
Surface area43140 Å2
MethodPISA
6
U: Glyceraldehyde-3-phosphate dehydrogenase
V: Glyceraldehyde-3-phosphate dehydrogenase
W: Glyceraldehyde-3-phosphate dehydrogenase
X: Glyceraldehyde-3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,9738
Polymers147,3194
Non-polymers2,6544
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19550 Å2
ΔGint-122 kcal/mol
Surface area41890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.534, 137.842, 157.786
Angle α, β, γ (deg.)85.95, 77.63, 86.88
Int Tables number1
Space group name H-MP1

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Components

#1: Protein ...
Glyceraldehyde-3-phosphate dehydrogenase


Mass: 36829.789 Da / Num. of mol.: 24 / Fragment: residues 24-357
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae NCCP11945 (bacteria)
Gene: NGK_2321 / Plasmid: NegoA.00617.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: B4RPP8, Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor
#2: Chemical...
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 756 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.35 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Berkeley D8 : 25% PEG 3350, 0.10M MES pH 5.5, 5% iso-Propanol, 0.10M ammonium citrate dibasic. NegoA.00617.a.B1.PS38018 at 8 mg/mL. plate 20061 D8 drop 1, Puck: PSL-2202, Cryo: 80% crystallant + 20% PEG 200

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Jun 28, 2025
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.3→49.02 Å / Num. obs: 374646 / % possible obs: 97.4 % / Redundancy: 3.5 % / CC1/2: 0.977 / Rmerge(I) obs: 0.208 / Rpim(I) all: 0.13 / Rrim(I) all: 0.246 / Χ2: 0.89 / Net I/σ(I): 7.3 / Num. measured all: 1327731
Reflection shellResolution: 2.3→2.36 Å / % possible obs: 97.2 % / Redundancy: 3.5 % / Rmerge(I) obs: 1.008 / Num. measured all: 96270 / Num. unique obs: 27683 / CC1/2: 0.519 / Rpim(I) all: 0.64 / Rrim(I) all: 1.199 / Χ2: 0.96 / Net I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
PHENIX(dev_5438: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→48.53 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 25.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2316 18761 5.01 %
Rwork0.1939 --
obs0.1958 374549 97.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→48.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms58784 0 1066 756 60606
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00560801
X-RAY DIFFRACTIONf_angle_d0.73582736
X-RAY DIFFRACTIONf_dihedral_angle_d13.02522792
X-RAY DIFFRACTIONf_chiral_restr0.0499804
X-RAY DIFFRACTIONf_plane_restr0.00710632
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.330.32516030.278411879X-RAY DIFFRACTION97
2.33-2.350.33395860.267311902X-RAY DIFFRACTION97
2.35-2.380.3246220.265911747X-RAY DIFFRACTION97
2.38-2.410.30636370.26411808X-RAY DIFFRACTION97
2.41-2.440.31646360.261311836X-RAY DIFFRACTION97
2.44-2.480.30416120.250611863X-RAY DIFFRACTION97
2.48-2.510.30986720.243211826X-RAY DIFFRACTION97
2.51-2.550.30186200.246311850X-RAY DIFFRACTION97
2.55-2.590.2935780.243211848X-RAY DIFFRACTION97
2.59-2.630.29556060.251611678X-RAY DIFFRACTION96
2.63-2.680.30316130.24311705X-RAY DIFFRACTION96
2.68-2.730.26835950.217311970X-RAY DIFFRACTION98
2.73-2.780.2795990.218911920X-RAY DIFFRACTION98
2.78-2.840.26716240.207511844X-RAY DIFFRACTION98
2.84-2.90.27536590.21911845X-RAY DIFFRACTION98
2.9-2.970.2616300.212311973X-RAY DIFFRACTION98
2.97-3.040.2626320.216711842X-RAY DIFFRACTION98
3.04-3.120.25666130.224511925X-RAY DIFFRACTION98
3.12-3.210.25636540.217911898X-RAY DIFFRACTION98
3.21-3.320.24536330.201511887X-RAY DIFFRACTION98
3.32-3.440.23936140.197511883X-RAY DIFFRACTION98
3.44-3.570.2276670.197711903X-RAY DIFFRACTION98
3.57-3.740.22626270.184411869X-RAY DIFFRACTION97
3.74-3.930.21016470.174711879X-RAY DIFFRACTION97
3.93-4.180.18556840.149111796X-RAY DIFFRACTION98
4.18-4.50.15886220.137811801X-RAY DIFFRACTION97
4.5-4.950.17455870.14111891X-RAY DIFFRACTION97
4.95-5.670.18166420.152611705X-RAY DIFFRACTION96
5.67-7.140.21015810.174612102X-RAY DIFFRACTION99
7.14-48.530.17256660.166711913X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.04360.09810.00170.1642-0.01520.1615-0.0515-0.0792-0.00950.0610.0009-0.14350.11940.0649-00.20810.0404-0.02040.33570.02190.300254.0478100.596966.4135
20.1022-0.1031-0.02890.1328-0.04520.0373-0.0540.0343-0.0692-0.090.0633-0.1296-0.00040.0044-00.21470.00110.0340.3566-0.02350.253450.4843108.821342.2155
30.0749-0.0473-0.03680.05320.00980.0647-0.1004-0.0410.1840.0322-0.02910.0784-0.2821-0.1083-0.03250.2603-0.0144-0.07490.37240.03440.305316.4022141.442244.2749
40.0299-0.00720.04020.0019-0.01840.1378-0.15560.13920.1823-0.13680.12630.1095-0.1626-0.12440.00020.3268-0.0647-0.10190.40820.08550.220920.6633137.698826.564
50.1409-0.00210.00910.2354-0.03960.1334-0.12760.08020.0229-0.11790.0987-0.03590.01870.0015-0.01230.221-0.0677-0.02530.36160.03970.189840.4134129.397735.0196
60.039-0.0194-0.00180.0578-0.06220.0575-0.09580.15930.193-0.03440.00870.0229-0.13750.1707-00.2227-0.0126-0.0650.331-0.00160.319348.353142.737563.3053
70.2077-0.00220.05830.23050.09260.1681-0.0853-0.06530.07370.11950.04360.04820.00690.0128-0.01880.20610.0408-0.04190.3187-0.03410.240133.2773134.279176.8698
80.0088-0.0198-0.00820.02340.010.029-0.10550.2634-0.02650.01680.06180.03840.04180.2175-00.2568-0.0118-0.00230.33670.00390.24116.775799.122347.872
90.02180.00760.0210.0224-0.01640.0529-0.12960.0524-0.01270.0172-0.1471-0.0453-0.04290.0714-0.00290.20890.03580.03530.3503-0.06570.276124.536697.606144.2409
100.28670.1159-0.11820.1914-0.05730.1968-0.05430.0069-0.04220.08760.03790.11390.018-0.00280.00030.17720.01380.0110.26610.00280.249213.8263108.774465.7416
110.025-0.00970.00840.0050.00410.0128-0.0584-0.0386-0.1188-0.14260.14940.0198-0.0431-0.02520.00040.5522-0.13590.09340.2749-0.03330.253391.6984119.0442-20.0371
120.01310.00830.01070.0181-0.00710.01460.0197-0.0164-0.1211-0.22250.14830.0013-0.0185-0.09190.00220.4556-0.06940.06770.2734-0.05480.284491.4068106.7855-18.412
130.00310.0009-0.00270.00290.0050.00030.05230.01850.0071-0.1632-0.0338-0.0889-0.0143-0.0436-00.7847-0.12850.15330.3931-0.08380.3804101.5538115.3376-25.0606
140.00650.0125-0.00030.0194-0.0120.0049-0.11670.01310.1323-0.24480.1726-0.0998-0.03370.048900.577-0.13020.1650.3474-0.0780.4525104.668124.5302-19.1546
150.0137-0.00310.01210.00460.0030.0253-0.11250.0192-0.0353-0.0464-0.0795-0.16090.00140.0461-0.02140.4513-0.16420.09460.2827-0.01530.3071101.748130.8368-14.1522
160.04990.01310.03190.02460.00350.0148-0.0563-0.0286-0.0276-0.0570.1121-0.0967-0.13350.1178-00.3913-0.04750.04790.2827-0.01210.305591.5885134.1623-1.7371
170.00180.00010.00250.00220.0021-0.0020.0506-0.01470.0248-0.08650.09390.0146-0.0267-0.163900.2823-0.05020.10640.2475-0.0830.3865104.7646111.34493.9428
180.06470.05630.02880.046-0.00380.05610.0417-0.0179-0.0278-0.1176-0.0069-0.0106-0.06390.021700.3327-0.02940.02350.2833-0.03190.268994.2758127.70037.4525
190.0056-0.00330.00530.0028-0.00130.0040.07520.11410.0589-0.13350.05940.0078-0.0875-0.062400.34280.00380.02070.29990.02910.356276.6571130.75824.1982
20-0.0057-0.00560.00420.0198-0.01590.0099-0.0157-0.092-0.03460.02880.16870.0773-0.007-0.1261-00.3369-0.02660.02410.2796-0.01610.304881.229126.48657.615
210.03610.04380.00930.03340.00830.0091-0.108-0.02120.1397-0.04980.08620.03220.040.0722-00.407-0.03370.00370.279-0.00120.243888.0659127.9846-4.1766
220.156-0.02070.06490.0790.01340.1435-0.0495-0.0907-0.13790.0307-0.0342-0.0208-0.0846-0.0888-0.00190.21580.015-0.02250.348-0.01920.263683.624798.027236.5357
230.04740.0630.02430.1609-0.21990.2201-0.0008-0.0152-0.02490.04510.0095-0.0642-0.0621-0.0098-00.2651-0.0214-0.04130.2413-0.04390.233492.6714119.172326.1829
240.122-0.13230.15050.195-0.20280.2345-0.12540.0706-0.1254-0.11550.1617-0.705-0.08250.1412-0.02940.2913-0.07310.12220.3588-0.11770.8241119.204498.72999.8112
250.0289-0.0068-0.02680.0089-0.0070.03660.02350.02120.0407-0.07130.0024-0.1678-0.02570.02990.01770.17760.03090.36030.3158-0.29450.8233118.297880.87051.8486
260.01710.02860.05990.02490.03360.0427-0.0207-0.0035-0.0341-0.20950.018-0.23070.00250.1163-00.3483-0.02390.08720.2981-0.05810.335998.194185.3519-1.359
270.0557-0.0880.02510.1144-0.0337-0.0088-0.1248-0.0663-0.0543-0.0940.1302-0.24980.10440.0291-0.00010.2744-0.02140.05620.2634-0.06130.36398.355378.429611.1824
280.0349-0.0834-0.02530.10630.03040.11570.0839-0.00390.0928-0.06950.01590.2205-0.1029-0.04050.00020.2697-0.011-0.06540.28290.03540.235560.0124104.38454.3011
290.07520.0365-0.04450.0892-0.05720.0447-0.0528-0.04940.0281-0.19360.11550.07380.1899-0.07020.02160.3602-0.0634-0.09790.32280.00460.244267.431283.8536-3.6215
30-0.001-0.0014-0.00140.00340.00550.0073-0.02450.0180.0237-0.11520.05630.1345-0.0245-0.146-00.2254-0.0064-0.00060.2871-0.02650.291879.807593.924416.3131
310.0628-0.05630.07780.1095-0.06340.0588-0.0303-0.08340.0079-0.24850.0306-0.04450.08310.0445-00.4014-0.048-0.02760.2679-0.03120.218580.718882.6955-3.3508
320.3164-0.14550.05970.45240.13110.1156-0.15630.05110.1144-0.42490.1685-0.1770.0620.02820.00450.4581-0.0428-0.00110.2862-0.01330.197977.929389.9167-9.7447
330.0141-0.0105-0.00060.00370.00450.0089-0.01070.11320.0059-0.00480.0572-0.09490.0388-0.0313-00.23690.0273-0.05880.2986-0.02090.4738126.339933.032882.989
340.01410.00650.00560.00860.01560.0117-0.02220.02920.12690.14120.011-0.1766-0.0757-0.038200.29750.0065-0.05130.3420.00440.4342125.240745.346382.7805
350.0182-0.0043-0.00350.0066-0.0030.0027-0.1073-0.0823-0.0981-0.07880.0058-0.11490.02460.046200.310.00330.00370.4634-0.00570.5416133.076235.958973.9816
360.00590.00040.01570.00810.01870.0318-0.09870.0171-0.0675-0.15750.1287-0.29050.13380.020.00020.27880.06380.0060.3051-0.04370.488125.022125.052571.1832
370.0276-0.00060.03330.01160.07220.2202-0.02650.0041-0.11950.21620.05780.1428-0.00650.1352-0.00310.25590.06160.04780.2510.00660.4777107.237818.930280.6923
38-0.00030.0029-0.00260.0035-0.01160.0117-0.0148-0.0529-0.0270.01040.0466-0.0810.1341-0.0192-00.26180.0017-0.02050.2595-0.02350.3124105.588741.220565.9202
390.12470.04260.130.03750.08240.1622-0.19870.0855-0.16150.090.14740.14520.06370.0937-0.01090.29920.02120.060.2709-0.03030.462299.051425.730476.3258
400.00260.0013-0.00880.0145-0.03040.0829-0.0138-0.0146-0.06360.1087-0.01680.0608-0.0575-0.0082-0.01190.42880.11920.16050.20840.10010.520199.189823.328594.3617
410.0042-0.0246-0.01150.02480.05660.0949-0.1575-0.07870.01230.37080.09520.18790.1850.1153-0.00910.32340.05520.05720.29690.02420.4906104.529826.149486.3618
420.0312-0.00340.02860.0372-0.0070.03430.10580.0168-0.073-0.0881-0.00570.1363-0.1785-0.069900.30740.04020.03780.3380.03920.359872.349761.142978.9978
430.1173-0.1478-0.03490.0901-0.08330.1626-0.06010.0245-0.21670.07470.04190.19970.0477-0.0552-0.00040.2524-0.01170.04060.3056-0.00320.524178.775236.88276.2867
440.06440.04580.06620.02620.04890.0427-0.098-0.0046-0.1509-0.54720.1186-0.1158-0.13150.0896-0.00020.4758-0.0192-0.01680.3139-0.06740.3339100.450251.649350.7713
450.04420.223-0.01410.5333-0.0530.1253-0.0560.03170.0005-0.17160.0491-0.19150.01980.0142-0.00220.24240.00250.03170.2512-0.00970.2829107.36469.505765.5563
460.11440.00410.03240.0575-0.00320.05510.05980.0081-0.04550.2481-0.14840.0214-0.05610.0472-00.46940.02080.02640.34960.02090.3698.293152.6923109.855
470.0414-0.0291-0.03520.2329-0.09070.0765-0.01760.0319-0.00550.1648-0.0107-0.0431-0.02840.0421-00.3221-0.0204-0.05860.29410.00480.2843110.660667.047793.4971
480.16230.0307-0.06310.08370.14180.3503-0.1143-0.0299-0.06020.53740.1713-0.00290.1631-0.13450.20461.01280.20670.20140.257-0.02540.107977.9041122.0269132.0177
490.62290.09590.0620.10530.0630.0664-0.18210.05410.14020.35650.16780.1383-0.0575-0.1068-0.23480.53010.13910.08450.2223-0.01590.269774.428137.8689118.7422
50-00.0037-0.004-0.0006-0.00190.0099-0.1098-0.02050.0280.1931-0.06280.01810.113-0.0059-00.3340.04770.13760.26830.01180.369666.8254117.3891108.1671
510.0943-0.197-0.1370.23490.20680.1924-0.02140.04770.03360.10250.0994-0.1501-0.0032-0.0287-0.00450.33710.0618-0.00250.2292-0.01020.255984.8461133.8058106.3953
520.10160.0244-0.0020.15370.12070.251-0.03150.0477-0.0997-0.0259-0.0333-0.0077-0.0876-0.0487-0.00330.24050.0182-0.03660.2605-0.00650.206187.8102102.251476.1633
530.081-0.0794-0.02530.23820.19550.15410.05320.0186-0.0427-0.1464-0.06290.0459-0.0371-0.032400.26720.067-0.05060.2452-0.00920.225979.0411122.786986.7971
540.0016-0.01220.01650.0468-0.05610.0666-0.0759-0.0272-0.0590.06090.11340.0616-0.0246-0.1255-0.01370.37940.00360.29170.3931-0.01460.90753.2796101.9886102.6052
550.00820.0050.00260.0054-0.00670.0088-0.03420.0588-0.02570.0142-0.05780.1326-0.0732-0.0009-00.29960.00610.0510.3497-0.07330.576361.0365109.413497.0156
560.0178-0.0028-0.00060.0034-0.0040.00140.0245-0.0892-0.03480.12990.18980.1042-0.0467-0.133200.45950.08470.05970.5139-0.03630.921246.3051107.0292101.8448
570.002-0.0015-0.00320.00340.00530.01350.0068-0.0277-0.04160.04450.05010.0449-0.0346-0.16450.05220.6160.15990.61920.6640.15760.982749.602296.6089115.5547
580.02260.0394-0.02090.0694-0.03310.01560.0490.024-0.0284-0.01260.1133-0.02960.02-0.14520.12220.5983-0.22130.64770.43450.16121.011354.169884.3226113.2045
590.0651-0.03130.06430.1324-0.07510.1398-0.2356-0.0305-0.24350.41380.03440.33050.124-0.0536-0.49620.77640.02380.3580.16530.06010.476173.538590.8274116.435
600.11380.09690.08530.0920.08630.3845-0.02740.0533-0.04840.4538-0.03970.58050.18760.0094-0.01590.4495-0.03380.15150.23900.50272.741684.6395104.3702
610.55620.124-0.42670.0208-0.09280.37520.06190.2608-0.13530.33670.0014-0.5231-0.1461-0.11790.16910.42110.1253-0.33930.27-0.13540.4149106.9747113.0652111.6456
620.04070.0001-0.06080.0149-0.02640.1441-0.1284-0.0127-0.14430.1278-0.2399-0.1549-0.16360.0214-0.03920.49640.0196-0.22470.3441-0.16090.9132116.6071114.3026107.7118
630.05810.0238-0.07470.02910.01230.2157-0.05830.02470.05350.0566-0.1019-0.2290.11440.0929-0.08980.55070.2443-0.27050.3347-0.06670.76113.849195.9817109.7781
640.1194-0.0596-0.01270.0237-0.01390.0207-0.02530.014-0.01760.57220.1087-0.37180.20640.02230.1291.0820.3723-0.4110.14240.01560.3515100.498689.8137122.2936
650.3620.0627-0.13720.0639-0.01550.1741-0.0910.0902-0.03350.72760.15-0.21380.2919-0.07250.13310.75670.1533-0.070.12480.02540.207690.894992.3344113.5094
660.0013-0.0054-0.01460.0731-0.01490.07110.0306-0.00970.00080.2020.01080.0010.1265-0.10.06551.11630.2287-0.06510.0792-0.16910.099990.3952101.8509126.8094
670.3814-0.12230.21610.3019-0.26540.2532-0.18450.01690.00170.2032-0.05320.09990.0904-0.0392-0.07910.86830.05820.11130.2928-0.03810.245484.694789.4287124.6277
680.055-0.01370.02120.0075-0.02060.0639-0.00930.01910.01080.04-0.0234-0.0373-0.03480.0089-0.06620.8190.2898-0.6850.3686-0.14510.3682108.8998100.9809121.3204
690.0104-0.0032-0.00620.0012-0.00510.00970.04990.10350.14120.0580.0597-0.0705-0.0014-0.0942-00.28710.03530.04720.34030.06250.401539.807162.2487108.885
700.0137-0.0136-0.00340.01750.00240.01140.15550.06110.2079-0.0042-0.01360.09740.0953-0.042200.26310.01570.01470.31120.02880.381731.067757.7049116.4179
710.12960.0499-0.13320.04490.02110.13170.01610.21870.0183-0.12850.0239-0.08460.03130.0438-00.30640.00410.06170.36660.01570.309549.540654.3418102.5299
720.0209-0.0059-0.03850.0050.00630.0363-0.06270.13940.008-0.16130.0566-0.00150.1552-0.027-00.32360.02030.04470.3543-0.00280.283150.719438.0279111.5707
730.04040.0032-0.01030.0082-0.01580.09420.0266-0.06960.12020.0674-0.0039-0.0343-0.02640.1191-00.25410.01770.02660.3521-0.0120.334564.469449.9439121.2214
740.0106-0.0004-0.01730.00460.01620.02460.07570.01370.0637-0.10920.0686-0.0097-0.00570.063300.27320.01120.05250.33050.01280.343356.457254.8667112.9502
750.2971-0.21970.02580.3327-0.01750.0418-0.1414-0.4164-0.27040.12030.09680.1220.32940.1104-0.03760.47880.1148-0.02090.45830.03280.225153.870519.25149.89
760.02680.00340.00220.0046-0.00690.00470.0739-0.207-0.03190.0350.0698-0.15870.0529-0.04560.00740.40060.1639-0.09330.3853-0.05460.334571.446819.4933142.0692
770.06120.0459-0.02810.0944-0.0750.04750.0041-0.01990.08930.00140.0253-0.11070.17030.077500.35680.08370.00830.3426-0.02510.295163.567628.5781126.1092
780.07850.07150.01740.11360.02740.0542-0.13890.3239-0.2641-0.08220.0732-0.08990.3282-0.0374-0.01040.4666-0.08910.01970.3632-0.06080.203732.936916.3349112.4032
790.19560.0144-0.03030.12960.0380.15870.05360.04430.08880.10220.03360.09970.1823-0.11640.0010.3382-0.102-0.0030.36070.01210.269420.260127.8126130.5044
800.0494-0.05170.05780.461-0.27940.22590.0451-0.04330.2046-0.19580.0795-0.04930.11180.27630.02740.1885-0.00710.04060.3505-0.08950.388552.186660.9127146.2477
810.1624-0.0888-0.18710.09340.21160.43390.020.00640.10360.08210.0580.08490.0275-0.0480.00060.2577-0.00030.04980.2871-0.03330.313129.392652.0672146.5144
820.22660.06920.11660.05120.04380.6479-0.09560.0244-0.5044-0.01240.01670.0061-0.07570.0446-0.02930.22370.00240.04560.2529-0.02990.481487.94752.724722.8324
830.52570.2717-0.11720.3556-0.11350.0742-0.54920.0854-0.8254-0.35220.0703-1.11190.2836-0.013-0.87370.30870.04750.159-0.00940.14311.053674.604832.68930.981
840.0782-0.0565-0.07970.27350.25240.24630.0132-0.0286-0.0032-0.0430.24510.1014-0.04770.05280.08640.3333-0.1054-0.06930.3670.180.354933.326731.006523.5812
850.0049-0.0251-0.02060.10620.06420.0508-0.1799-0.0460.1062-0.21060.32950.449-0.0811-0.05140.00280.2918-0.0782-0.09950.43750.18210.511429.039737.739824.9797
860.00440.00660.00180.15320.14750.1646-0.1231-0.0238-0.13560.13480.32410.1370.1572-0.13820.02430.2615-0.04630.02420.33670.1190.403832.732223.084536.051
870.1365-0.02340.12030.0136-0.06250.532-0.09420.0364-0.2556-0.44360.1322-0.48010.14-0.1456-0.00620.4115-0.10080.18760.2673-0.02110.651750.186216.328626.8234
880.0047-0.00390.00370.00360.00370.005-0.06410.0735-0.02730.0546-0.1423-0.03770.0765-0.153-00.28090.00750.02190.31480.05160.346752.257940.055439.0504
890.0337-0.01190.10130.0088-0.04870.2916-0.1032-0.0559-0.31730.0094-0.1288-0.0688-0.0443-0.083-0.03350.2985-0.00850.10490.25730.02490.491555.730424.162233.7637
900.13850.03080.24540.0260.0780.5969-0.21830.0921-0.2799-0.19610.0089-0.290.0304-0.019-0.31150.2676-0.0250.23120.2173-0.01130.568561.168622.93926.6785
910.0039-0.001-0.0119-0.00170.00010.0378-0.10020.0165-0.0821-0.08310.0192-0.12450.1398-0.0466-0.06020.7396-0.34110.71510.4058-0.20090.554558.109119.416712.5079
920.2022-0.00210.25290.0233-0.0760.2881-0.186-0.1101-0.22-0.6730.1488-0.57130.0419-0.0076-0.13820.4513-0.17590.24030.2822-0.02510.604152.101722.823320.3373
930.0018-0.01010.00780.0555-0.02190.01560.0559-0.0220.0331-0.2544-0.0043-0.0398-0.02430.11480.0481.136-0.49520.23890.5716-0.03060.264855.865244.0877-3.8843
940.0189-0.00940.01770.0660.02540.0306-0.03890.0126-0.0309-0.08940.03490.0081-0.03560.0431-0.00570.8108-0.56990.09250.3583-0.18420.261355.898936.69224.4305
950.1083-0.03770.02470.0936-0.09420.1075-0.05630.05530.055-0.0964-0.0327-0.05030.01620.0153-0.0660.9915-0.38740.17270.3591-0.24870.577360.827137.6057-8.4435
960.0338-0.00850.01630.0114-0.0110.0106-0.0169-0.01690.0608-0.056-0.0169-0.02950.05330.003-0.01341.0882-0.56550.2350.6551-0.05560.637158.150957.6502-4.5734
970.31210.1332-0.05960.6208-0.24060.5636-0.37420.25920.0282-0.86940.61650.06920.2772-0.17141.46280.4541-0.2342-0.29260.4240.31410.122745.907962.424510.0608
980.0076-0.00580.00620.00040.00440.0094-0.10690.04950.01640.269-0.032-0.0682-0.09680.00700.65470.0372-0.04010.3570.04370.23358.232458.707452.9929
990.013-0.0095-0.00630.00180.00240.01950.02950.0372-0.12830.3215-0.0942-0.06270.0405-0.076-0.00280.51630.002-0.11260.35590.06880.310961.181948.471250.7538
1000.01470.00450.01030.0024-0.00330.0112-0.0895-0.08530.00930.2072-0.01370.1546-0.0041-0.055-0.00010.96220.23660.33530.59030.12550.526143.616157.994756.3886
1010.00170.004-0.00260.0249-0.01390.01070.0426-0.05580.06860.0928-0.06320.06650.0246-0.0501-0.01590.7920.20090.3610.4790.04290.408543.701867.195251.435
1020.37810.0963-0.01470.0398-0.01320.004-0.09570.03180.26480.25960.16030.2668-0.0636-0.12780.00450.4490.09480.10870.22850.01320.288849.194774.567637.7201
1030.06910.0336-0.0120.0397-0.04520.0249-0.0509-0.00190.07770.34390.22560.3984-0.0065-0.1518-00.28620.0250.06030.33150.06930.359345.380763.028129.1637
1040.01950.0078-0.01240.00760.00260.0054-0.06860.07390.00950.16760.00190.0044-0.0668-0.003400.35450.0311-0.05350.3017-0.02230.300762.952676.319428.619
1050.10280.10890.08450.09520.05360.1103-0.0350.10850.10230.28690.09840.1852-0.05650.12450.01580.36410.03730.00920.26990.02840.298556.643270.272333.0098
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 119 )
2X-RAY DIFFRACTION2chain 'A' and (resid 120 through 334 )
3X-RAY DIFFRACTION3chain 'B' and (resid 2 through 84 )
4X-RAY DIFFRACTION4chain 'B' and (resid 85 through 150 )
5X-RAY DIFFRACTION5chain 'B' and (resid 151 through 334 )
6X-RAY DIFFRACTION6chain 'C' and (resid 2 through 69 )
7X-RAY DIFFRACTION7chain 'C' and (resid 70 through 333 )
8X-RAY DIFFRACTION8chain 'D' and (resid 2 through 46 )
9X-RAY DIFFRACTION9chain 'D' and (resid 47 through 69 )
10X-RAY DIFFRACTION10chain 'D' and (resid 70 through 333 )
11X-RAY DIFFRACTION11chain 'E' and (resid 1 through 33 )
12X-RAY DIFFRACTION12chain 'E' and (resid 34 through 67 )
13X-RAY DIFFRACTION13chain 'E' and (resid 68 through 84 )
14X-RAY DIFFRACTION14chain 'E' and (resid 85 through 111 )
15X-RAY DIFFRACTION15chain 'E' and (resid 112 through 129 )
16X-RAY DIFFRACTION16chain 'E' and (resid 130 through 179 )
17X-RAY DIFFRACTION17chain 'E' and (resid 180 through 199 )
18X-RAY DIFFRACTION18chain 'E' and (resid 200 through 254 )
19X-RAY DIFFRACTION19chain 'E' and (resid 255 through 278 )
20X-RAY DIFFRACTION20chain 'E' and (resid 279 through 303 )
21X-RAY DIFFRACTION21chain 'E' and (resid 304 through 333 )
22X-RAY DIFFRACTION22chain 'F' and (resid 2 through 129 )
23X-RAY DIFFRACTION23chain 'F' and (resid 130 through 334 )
24X-RAY DIFFRACTION24chain 'G' and (resid 4 through 111 )
25X-RAY DIFFRACTION25chain 'G' and (resid 112 through 150 )
26X-RAY DIFFRACTION26chain 'G' and (resid 151 through 249 )
27X-RAY DIFFRACTION27chain 'G' and (resid 250 through 333 )
28X-RAY DIFFRACTION28chain 'H' and (resid 2 through 111 )
29X-RAY DIFFRACTION29chain 'H' and (resid 112 through 179 )
30X-RAY DIFFRACTION30chain 'H' and (resid 180 through 199 )
31X-RAY DIFFRACTION31chain 'H' and (resid 200 through 265 )
32X-RAY DIFFRACTION32chain 'H' and (resid 266 through 333 )
33X-RAY DIFFRACTION33chain 'I' and (resid 1 through 33 )
34X-RAY DIFFRACTION34chain 'I' and (resid 34 through 67 )
35X-RAY DIFFRACTION35chain 'I' and (resid 68 through 84 )
36X-RAY DIFFRACTION36chain 'I' and (resid 85 through 129 )
37X-RAY DIFFRACTION37chain 'I' and (resid 130 through 179 )
38X-RAY DIFFRACTION38chain 'I' and (resid 180 through 199 )
39X-RAY DIFFRACTION39chain 'I' and (resid 200 through 254 )
40X-RAY DIFFRACTION40chain 'I' and (resid 255 through 278 )
41X-RAY DIFFRACTION41chain 'I' and (resid 279 through 333 )
42X-RAY DIFFRACTION42chain 'J' and (resid 2 through 95 )
43X-RAY DIFFRACTION43chain 'J' and (resid 96 through 334 )
44X-RAY DIFFRACTION44chain 'K' and (resid 2 through 84 )
45X-RAY DIFFRACTION45chain 'K' and (resid 85 through 333 )
46X-RAY DIFFRACTION46chain 'L' and (resid 2 through 129 )
47X-RAY DIFFRACTION47chain 'L' and (resid 130 through 333 )
48X-RAY DIFFRACTION48chain 'M' and (resid 1 through 84 )
49X-RAY DIFFRACTION49chain 'M' and (resid 85 through 179 )
50X-RAY DIFFRACTION50chain 'M' and (resid 180 through 199 )
51X-RAY DIFFRACTION51chain 'M' and (resid 200 through 334 )
52X-RAY DIFFRACTION52chain 'N' and (resid 1 through 150 )
53X-RAY DIFFRACTION53chain 'N' and (resid 151 through 334 )
54X-RAY DIFFRACTION54chain 'O' and (resid 3 through 37 )
55X-RAY DIFFRACTION55chain 'O' and (resid 38 through 57 )
56X-RAY DIFFRACTION56chain 'O' and (resid 58 through 91 )
57X-RAY DIFFRACTION57chain 'O' and (resid 92 through 124 )
58X-RAY DIFFRACTION58chain 'O' and (resid 125 through 150 )
59X-RAY DIFFRACTION59chain 'O' and (resid 151 through 254 )
60X-RAY DIFFRACTION60chain 'O' and (resid 255 through 333 )
61X-RAY DIFFRACTION61chain 'P' and (resid 3 through 56 )
62X-RAY DIFFRACTION62chain 'P' and (resid 57 through 88 )
63X-RAY DIFFRACTION63chain 'P' and (resid 89 through 129 )
64X-RAY DIFFRACTION64chain 'P' and (resid 130 through 179 )
65X-RAY DIFFRACTION65chain 'P' and (resid 180 through 265 )
66X-RAY DIFFRACTION66chain 'P' and (resid 266 through 295 )
67X-RAY DIFFRACTION67chain 'P' and (resid 296 through 316 )
68X-RAY DIFFRACTION68chain 'P' and (resid 317 through 333 )
69X-RAY DIFFRACTION69chain 'Q' and (resid 1 through 33 )
70X-RAY DIFFRACTION70chain 'Q' and (resid 34 through 67 )
71X-RAY DIFFRACTION71chain 'Q' and (resid 68 through 179 )
72X-RAY DIFFRACTION72chain 'Q' and (resid 180 through 227 )
73X-RAY DIFFRACTION73chain 'Q' and (resid 228 through 303 )
74X-RAY DIFFRACTION74chain 'Q' and (resid 304 through 333 )
75X-RAY DIFFRACTION75chain 'R' and (resid 2 through 111 )
76X-RAY DIFFRACTION76chain 'R' and (resid 112 through 150 )
77X-RAY DIFFRACTION77chain 'R' and (resid 151 through 334 )
78X-RAY DIFFRACTION78chain 'S' and (resid 2 through 95 )
79X-RAY DIFFRACTION79chain 'S' and (resid 96 through 333 )
80X-RAY DIFFRACTION80chain 'T' and (resid 2 through 84 )
81X-RAY DIFFRACTION81chain 'T' and (resid 85 through 333 )
82X-RAY DIFFRACTION82chain 'U' and (resid 1 through 150 )
83X-RAY DIFFRACTION83chain 'U' and (resid 151 through 333 )
84X-RAY DIFFRACTION84chain 'V' and (resid 2 through 23 )
85X-RAY DIFFRACTION85chain 'V' and (resid 24 through 84 )
86X-RAY DIFFRACTION86chain 'V' and (resid 85 through 129 )
87X-RAY DIFFRACTION87chain 'V' and (resid 130 through 179 )
88X-RAY DIFFRACTION88chain 'V' and (resid 180 through 199 )
89X-RAY DIFFRACTION89chain 'V' and (resid 200 through 227 )
90X-RAY DIFFRACTION90chain 'V' and (resid 228 through 254 )
91X-RAY DIFFRACTION91chain 'V' and (resid 255 through 278 )
92X-RAY DIFFRACTION92chain 'V' and (resid 279 through 334 )
93X-RAY DIFFRACTION93chain 'W' and (resid 5 through 37 )
94X-RAY DIFFRACTION94chain 'W' and (resid 38 through 57 )
95X-RAY DIFFRACTION95chain 'W' and (resid 58 through 92 )
96X-RAY DIFFRACTION96chain 'W' and (resid 93 through 130 )
97X-RAY DIFFRACTION97chain 'W' and (resid 131 through 331 )
98X-RAY DIFFRACTION98chain 'X' and (resid 1 through 33 )
99X-RAY DIFFRACTION99chain 'X' and (resid 34 through 75 )
100X-RAY DIFFRACTION100chain 'X' and (resid 76 through 111 )
101X-RAY DIFFRACTION101chain 'X' and (resid 112 through 129 )
102X-RAY DIFFRACTION102chain 'X' and (resid 130 through 179 )
103X-RAY DIFFRACTION103chain 'X' and (resid 180 through 254 )
104X-RAY DIFFRACTION104chain 'X' and (resid 255 through 278 )
105X-RAY DIFFRACTION105chain 'X' and (resid 279 through 333 )

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About Yorodumi

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Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
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