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- PDB-3lyc: Crystal structure of Putative pectinase (YP_001304412.1) from Par... -

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Basic information

Entry
Database: PDB / ID: 3lyc
TitleCrystal structure of Putative pectinase (YP_001304412.1) from Parabacteroides distasonis ATCC 8503 at 2.30 A resolution
ComponentsPutative pectinase
KeywordsCELL ADHESION / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / Lipoprotein / Adhesion
Function / homologyPectate Lyase C-like - #120 / Putative auto-transporter adhesin, head GIN domain / Putative auto-transporter adhesin, head GIN domain / Pectate Lyase C-like / 3 Solenoid / Prokaryotic membrane lipoprotein lipid attachment site profile. / Mainly Beta / Putative lipoprotein
Function and homology information
Biological speciesParabacteroides distasonis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Putative pectinase (YP_001304412.1) from Parabacteroides distasonis ATCC 8503 at 2.30 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionFeb 26, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Nov 6, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id ..._pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative pectinase
B: Putative pectinase
C: Putative pectinase
D: Putative pectinase
E: Putative pectinase
F: Putative pectinase
G: Putative pectinase
H: Putative pectinase
I: Putative pectinase
J: Putative pectinase
K: Putative pectinase
L: Putative pectinase
M: Putative pectinase
N: Putative pectinase
O: Putative pectinase
P: Putative pectinase


Theoretical massNumber of molelcules
Total (without water)419,64216
Polymers419,64216
Non-polymers00
Water15,313850
1
A: Putative pectinase
B: Putative pectinase


Theoretical massNumber of molelcules
Total (without water)52,4552
Polymers52,4552
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1980 Å2
ΔGint-8 kcal/mol
Surface area19700 Å2
MethodPISA
2
C: Putative pectinase
D: Putative pectinase


Theoretical massNumber of molelcules
Total (without water)52,4552
Polymers52,4552
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1870 Å2
ΔGint-10 kcal/mol
Surface area19970 Å2
MethodPISA
3
E: Putative pectinase
F: Putative pectinase


Theoretical massNumber of molelcules
Total (without water)52,4552
Polymers52,4552
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2050 Å2
ΔGint-8 kcal/mol
Surface area19590 Å2
MethodPISA
4
G: Putative pectinase
H: Putative pectinase


Theoretical massNumber of molelcules
Total (without water)52,4552
Polymers52,4552
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1900 Å2
ΔGint-9 kcal/mol
Surface area20080 Å2
MethodPISA
5
I: Putative pectinase
J: Putative pectinase


Theoretical massNumber of molelcules
Total (without water)52,4552
Polymers52,4552
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-10 kcal/mol
Surface area19740 Å2
MethodPISA
6
K: Putative pectinase
L: Putative pectinase


Theoretical massNumber of molelcules
Total (without water)52,4552
Polymers52,4552
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1820 Å2
ΔGint-7 kcal/mol
Surface area19830 Å2
MethodPISA
7
M: Putative pectinase
N: Putative pectinase


Theoretical massNumber of molelcules
Total (without water)52,4552
Polymers52,4552
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1940 Å2
ΔGint-9 kcal/mol
Surface area19770 Å2
MethodPISA
8
O: Putative pectinase
P: Putative pectinase


Theoretical massNumber of molelcules
Total (without water)52,4552
Polymers52,4552
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-11 kcal/mol
Surface area19650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.116, 104.606, 393.587
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
31E
41G
51I
61K
71M
81O
12B
22D
32F
42H
52J
62L
72N
82P

NCS domain segments:

Refine code: 4

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLYGLYHISHISAA0 - 961 - 71
211GLYGLYHISHISCC0 - 961 - 71
311GLYGLYHISHISEE0 - 961 - 71
411GLYGLYHISHISGG0 - 961 - 71
511GLYGLYHISHISII0 - 961 - 71
611GLYGLYHISHISKK0 - 961 - 71
711GLYGLYHISHISMM0 - 961 - 71
811GLYGLYHISHISOO0 - 961 - 71
121PROPROGLUGLUAA101 - 26676 - 241
221PROPROGLUGLUCC101 - 26676 - 241
321PROPROGLUGLUEE101 - 26676 - 241
421PROPROGLUGLUGG101 - 26676 - 241
521PROPROGLUGLUII101 - 26676 - 241
621PROPROGLUGLUKK101 - 26676 - 241
721PROPROGLUGLUMM101 - 26676 - 241
821PROPROGLUGLUOO101 - 26676 - 241
112ASNASNPHEPHEBB30 - 935 - 68
212ASNASNPHEPHEDD30 - 935 - 68
312ASNASNPHEPHEFF30 - 935 - 68
412ASNASNPHEPHEHH30 - 935 - 68
512ASNASNPHEPHEJJ30 - 935 - 68
612ASNASNPHEPHELL30 - 935 - 68
712ASNASNPHEPHENN30 - 935 - 68
812ASNASNPHEPHEPP30 - 935 - 68
122PROPROGLUGLUBB101 - 26676 - 241
222PROPROGLUGLUDD101 - 26676 - 241
322PROPROGLUGLUFF101 - 26676 - 241
422PROPROGLUGLUHH101 - 26676 - 241
522PROPROGLUGLUJJ101 - 26676 - 241
622PROPROGLUGLULL101 - 26676 - 241
722PROPROGLUGLUNN101 - 26676 - 241
822PROPROGLUGLUPP101 - 26676 - 241

NCS ensembles :
ID
1
2

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Components

#1: Protein
Putative pectinase / Putative lipoprotein


Mass: 26227.631 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Parabacteroides distasonis (bacteria) / Strain: ATCC 8503 / DSM 20701 / NCTC 11152 / Gene: BDI_3084 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: A6LGH6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 850 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. THE CLONED CONSTRUCT CONTAINS RESIDUES 27-266 OF THE FULL LENGTH PROTEIN.

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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: 2.55 Å3/Da / Density % sol: 51.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 40.0000% Ethanol, 0.1170M magnesium chloride, 0.1M TRIS pH 8.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.97926,0.97882
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 9, 2009 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979261
30.978821
ReflectionResolution: 2.3→49.507 Å / Num. obs: 186629 / % possible obs: 97.3 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 37.716 Å2 / Rmerge(I) obs: 0.114 / Net I/σ(I): 8.64
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.3-2.380.6631.85675916841190.9
2.38-2.480.5762.16474618648194.1
2.48-2.590.4572.87227217852196.6
2.59-2.730.3613.89265719108198.4
2.73-2.90.27159354218597198.5
2.9-3.120.1996.89633818467198.9
3.12-3.430.12910.110185318747198.9
3.43-3.930.08314.910850719120198.7
3.93-4.930.06418.611418618929198.8
4.93-49.5070.06118.613741020160199.5

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0102refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→49.507 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.923 / Occupancy max: 1 / Occupancy min: 0.33 / SU B: 19.051 / SU ML: 0.208 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.411 / ESU R Free: 0.27
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. ANALYSIS OF THE PATTERSON FUNCTION USING XTRIAGE REVEALS A SIGNIFICANT OFF-ORIGIN PEAK THAT IS 63% OF THE ORIGIN PEAK INDICATING PSEUDO TRANSLATION SYMMETRY RELATING PAIRS OF DIMERS IN THE UNIT CELL. 5.ALTHOUGH THERE IS GENERAL AGREEMENT BETWEEN THE ELECTRON DENSITY MAPS AND THE MODEL MAPS, THE REASONS FOR THE ELEVATED R-FACTORS (R-WORK AND R-FREE) ARE NOT COMPLETELY UNDERSTOOD. 6. GLY 168 ON ALL 16 SUBUNITS IN THE ASYMMETRIC UNIT IS FLAGGED AS A MOLPROBITY RAMACHANDRAN OUTLIER EVEN THOUGH IT IS POSITIONED IN WELL DEFINED ELECTRON DENSITY. HIS A96 IS IN A DISORDERED REGION OF ELECTRON DENSITY AND ARE FLAGGED AS A RAMACHANDRAN OUTLIER IN MOLPROBITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.28 9370 5 %RANDOM
Rwork0.244 ---
obs0.246 186512 97.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 74.52 Å2 / Biso mean: 38.194 Å2 / Biso min: 11.14 Å2
Baniso -1Baniso -2Baniso -3
1--1.62 Å20 Å20 Å2
2--1.86 Å20 Å2
3----0.24 Å2
Refinement stepCycle: LAST / Resolution: 2.3→49.507 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28340 0 0 850 29190
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02229367
X-RAY DIFFRACTIONr_bond_other_d0.0010.0219497
X-RAY DIFFRACTIONr_angle_refined_deg0.771.95639715
X-RAY DIFFRACTIONr_angle_other_deg0.517348112
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.41353984
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.2326.141311
X-RAY DIFFRACTIONr_dihedral_angle_3_deg8.996155082
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.0051584
X-RAY DIFFRACTIONr_chiral_restr0.0620.24446
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0233787
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025533
X-RAY DIFFRACTIONr_mcbond_it0.711319063
X-RAY DIFFRACTIONr_mcbond_other0.20138068
X-RAY DIFFRACTIONr_mcangle_it1.438530493
X-RAY DIFFRACTIONr_scbond_it2.724810304
X-RAY DIFFRACTIONr_scangle_it4.424119133
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A2634MEDIUM POSITIONAL0.30.5
12C2634MEDIUM POSITIONAL0.250.5
13E2634MEDIUM POSITIONAL0.240.5
14G2634MEDIUM POSITIONAL0.260.5
15I2634MEDIUM POSITIONAL0.260.5
16K2634MEDIUM POSITIONAL0.290.5
17M2634MEDIUM POSITIONAL0.280.5
18O2634MEDIUM POSITIONAL0.310.5
11A2634MEDIUM THERMAL0.632
12C2634MEDIUM THERMAL0.562
13E2634MEDIUM THERMAL0.672
14G2634MEDIUM THERMAL0.612
15I2634MEDIUM THERMAL0.682
16K2634MEDIUM THERMAL0.562
17M2634MEDIUM THERMAL0.652
18O2634MEDIUM THERMAL0.552
21B2439MEDIUM POSITIONAL0.230.5
22D2439MEDIUM POSITIONAL0.290.5
23F2439MEDIUM POSITIONAL0.240.5
24H2439MEDIUM POSITIONAL0.270.5
25J2439MEDIUM POSITIONAL0.250.5
26L2439MEDIUM POSITIONAL0.330.5
27N2439MEDIUM POSITIONAL0.240.5
28P2439MEDIUM POSITIONAL0.270.5
21B2439MEDIUM THERMAL0.482
22D2439MEDIUM THERMAL0.42
23F2439MEDIUM THERMAL0.442
24H2439MEDIUM THERMAL0.432
25J2439MEDIUM THERMAL0.452
26L2439MEDIUM THERMAL0.442
27N2439MEDIUM THERMAL0.452
28P2439MEDIUM THERMAL0.462
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 623 -
Rwork0.305 12083 -
all-12706 -
obs--90.53 %
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.54040.13350.26540.28160.00150.5233-0.03520.12130.0393-0.01340.01830.0617-0.0085-0.05320.01690.1507-0.0097-0.00010.07710.01160.139775.8723-26.121982.6322
22.0146-0.31770.7820.6833-0.31131.72590.06370.0710.0077-0.0295-0.088-0.13070.20160.44780.02440.09920.05430.00750.19440.03830.0837103.7296-29.705664.654
32.9127-0.29290.10610.8675-0.03350.9559-0.01990.04550.1366-0.0071-0.0755-0.0474-0.08950.08690.09540.1646-0.0067-0.00390.17820.01830.088280.0009-26.425811.7256
42.0742-0.21821.0980.6382-0.06482.11020.0141-0.1954-0.02760.0015-0.03150.23770.0155-0.60390.01740.15540.0097-0.01070.3343-0.04810.121452.3899-26.264929.9994
51.71480.0346-0.30680.61170.09690.38140.00430.159-0.0993-0.0175-0.0255-0.0792-0.0060.01750.02120.11810.01120.00590.085-0.00480.137180.41140.718982.4386
62.0685-0.3752-0.64790.57050.27671.77460.04760.15170.02410.0157-0.08950.094-0.1154-0.44120.04190.12350.0487-0.00620.2042-0.03680.072552.34574.087164.7591
72.6538-0.4137-0.16590.6983-0.06380.9896-0.0420.0162-0.2455-0.03590.00330.11420.1173-0.07110.03870.1303-0.00020.02490.1807-0.02190.124176.64620.358811.8095
82.0173-0.0559-1.03430.8586-0.19842.07-0.048-0.24130.0051-0.05030.0393-0.17220.07150.58240.00870.07590.03370.02620.33260.02160.1006104.38920.723129.9449
91.6527-0.00380.12610.6311-0.03470.23240.01970.18870.0588-0.0268-0.03450.0689-0.0219-0.01170.01480.15280.0091-0.00010.0882-0.00650.111279.362926.591182.6333
102.1867-0.47030.56560.60190.01151.80550.05460.07670.00760.0541-0.0013-0.08480.07360.3749-0.05330.11780.0307-0.010.1744-0.00490.0634106.093523.221262.7927
112.1307-0.37560.1860.56780.1061.1556-0.04-0.10020.1065-0.05350.0409-0.0543-0.13960.0291-0.0010.142-0.0132-0.01770.1810.01360.102480.131125.909511.7567
122.8925-0.07161.21450.91960.17411.89420.0155-0.12470.02870.0198-0.06310.301-0.0143-0.58620.04750.03920.0203-0.01880.3795-0.03350.154253.163425.477631.1939
131.61630.0249-0.14310.43360.02850.31580.01390.1672-0.0496-0.0234-0.0083-0.06720.00080.0045-0.00560.1535-0.0070.00430.0766-0.00570.129377.024652.711182.2821
142.9252-0.4441-1.07040.8027-0.04581.87170.0710.1136-0.05050.0255-0.01840.1117-0.1591-0.4147-0.05260.09550.01920.00740.1967-0.01010.06449.963456.011362.9875
151.6602-0.2211-0.01110.7724-0.2111.07730.0037-0.1073-0.0225-0.0665-0.0676-0.00860.11360.01820.06390.1598-0.00190.01720.1885-0.0290.088376.354952.72111.6205
162.5701-0.0051-0.97221.0552-0.06441.83670.0831-0.1477-0.047-0.0154-0.1329-0.4919-0.03430.68470.04990.12840.00480.01340.42010.08440.2341103.060453.063231.6134
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 266
2X-RAY DIFFRACTION2B30 - 266
3X-RAY DIFFRACTION3C0 - 266
4X-RAY DIFFRACTION4D0 - 266
5X-RAY DIFFRACTION5E0 - 266
6X-RAY DIFFRACTION6F28 - 266
7X-RAY DIFFRACTION7G0 - 266
8X-RAY DIFFRACTION8H0 - 266
9X-RAY DIFFRACTION9I0 - 266
10X-RAY DIFFRACTION10J28 - 266
11X-RAY DIFFRACTION11K0 - 266
12X-RAY DIFFRACTION12L27 - 266
13X-RAY DIFFRACTION13M0 - 266
14X-RAY DIFFRACTION14N29 - 266
15X-RAY DIFFRACTION15O0 - 266
16X-RAY DIFFRACTION16P30 - 266

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  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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