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- PDB-4o9k: Crystal structure of the CBS pair of a putative D-arabinose 5-pho... -

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Basic information

Entry
Database: PDB / ID: 4o9k
TitleCrystal structure of the CBS pair of a putative D-arabinose 5-phosphate isomerase from Methylococcus capsulatus in complex with CMP-Kdo
ComponentsArabinose 5-phosphate isomerase
KeywordsISOMERASE / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC / CBS pair / CMP-Kdo binding / CMP-Kdo
Function / homology
Function and homology information


arabinose-5-phosphate isomerase / arabinose-5-phosphate isomerase activity / carbohydrate derivative metabolic process / carbohydrate derivative binding / carbohydrate metabolic process
Similarity search - Function
Phosphosugar isomerase, KdsD/KpsF-type / KpsF-like, SIS domain / SIS domain / CBS-domain / CBS-domain / SIS domain / SIS domain profile. / Domain in cystathionine beta-synthase and other proteins. / CBS domain / CBS domain ...Phosphosugar isomerase, KdsD/KpsF-type / KpsF-like, SIS domain / SIS domain / CBS-domain / CBS-domain / SIS domain / SIS domain profile. / Domain in cystathionine beta-synthase and other proteins. / CBS domain / CBS domain / CBS domain profile. / Roll / Alpha Beta
Similarity search - Domain/homology
Chem-CMK / Arabinose 5-phosphate isomerase
Similarity search - Component
Biological speciesMethylococcus capsulatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 Å
AuthorsShabalin, I.G. / Cooper, D.R. / Shumilin, I.A. / Zimmerman, M.D. / Majorek, K.A. / Hammonds, J. / Hillerich, B.S. / Nawar, A. / Bonanno, J. / Seidel, R. ...Shabalin, I.G. / Cooper, D.R. / Shumilin, I.A. / Zimmerman, M.D. / Majorek, K.A. / Hammonds, J. / Hillerich, B.S. / Nawar, A. / Bonanno, J. / Seidel, R. / Almo, S.C. / Minor, W. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: Crystal structure and kinetic properties of D-arabinose 5-phosphate isomerase from Methylococcus capsulatus
Authors: Shabalin, I.G. / Cooper, D.R. / Shumilin, I.A. / Zimmerman, M.D. / Majorek, K.A. / Hammonds, J. / Hillerich, B.S. / Nawar, A. / Bonanno, J. / Seidel, R. / Almo, S.C. / Minor, W.
History
DepositionJan 2, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Arabinose 5-phosphate isomerase
B: Arabinose 5-phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7525
Polymers28,5732
Non-polymers1,1793
Water3,729207
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4510 Å2
ΔGint-11 kcal/mol
Surface area11930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.151, 62.408, 75.664
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
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A204 - 330
2010B204 - 330

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Components

#1: Protein Arabinose 5-phosphate isomerase / API


Mass: 14286.727 Da / Num. of mol.: 2 / Fragment: CBS pair (UNP residues 201-330)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylococcus capsulatus (bacteria) / Strain: Bath / Gene: Locus tag MCA0746, MCA0746 / Plasmid: pSGC-His / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL
References: UniProt: Q60AU8, arabinose-5-phosphate isomerase
#2: Chemical ChemComp-CMK / CYTIDINE 5'-MONOPHOSPHATE 3-DEOXY-BETA-D-GULO-OCT-2-ULO-PYRANOSONIC ACID / CMP-2-KETO-3-DEOXY-OCTULOSONIC ACID


Mass: 543.373 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H26N3O15P
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 207 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE COMPLETE SEQUENCE (1-330) TOGETHER WITH THE HIS-TAG WAS USED IN CRYSTALLIZATION. THE PROTEIN ...THE COMPLETE SEQUENCE (1-330) TOGETHER WITH THE HIS-TAG WAS USED IN CRYSTALLIZATION. THE PROTEIN WAS INCUBATED WITH CHYMOTRYPSIN RIGHT BEFORE CRYSTALLIZATION, AND SUBJECTED TO THE LIMITED PROTEOLYSIS. THE COMPLETE LENGTH OF THE CRYSTALLIZED SEQUENCE IS UNKNOWN. THE REPORTED SEQUENCE IS THE ONE OBSERVED IN THE EXPERIMENT.

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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: 1.87 Å3/Da / Density % sol: 34.06 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 ul of 9 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide and 0.5 mM TCEP were mixed with 0.2 ul of the MCSG-II condition #27 (0.2 M Ammomium Acetate, 0.1 ...Details: 0.2 ul of 9 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide and 0.5 mM TCEP were mixed with 0.2 ul of the MCSG-II condition #27 (0.2 M Ammomium Acetate, 0.1 M HEPES:NaOH pH 7.5, 25% (w/v) PEG 3350) and equilibrated against 1.5 M NaCl solution in QIAGEN EasyXtal 15-Well Tool plate. Before crystallization protein was incubated with 1/50 v/v of 2 mg/ml chymotrypsin solution at 289 K for 3 hours, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 11, 2013 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionRedundancy: 5.7 % / Number: 106108 / Rmerge(I) obs: 0.146 / Χ2: 1.11 / D res high: 1.85 Å / D res low: 50 Å / Num. obs: 18460 / % possible obs: 98.6
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.025094.510.0763.0965.4
3.995.0298.110.0672.1415.6
3.483.9998.210.0881.6425.8
3.163.4898.310.1011.4725.8
2.943.1698.810.1141.4315.8
2.762.9498.410.1351.2165.8
2.632.7698.810.1381.0395.9
2.512.6398.510.1680.9835.9
2.412.5198.710.1830.9245.8
2.332.4198.810.1930.9015.9
2.262.3398.610.2190.8485.9
2.192.2698.910.2280.8335.8
2.142.1999.210.2670.8395.8
2.082.149910.3140.7535.8
2.042.0899.510.360.7565.8
1.992.0499.210.4220.7145.9
1.951.9999.310.5060.6745.8
1.921.9599.610.5710.6285.7
1.881.9299.610.6210.6485.6
1.851.8899.210.7030.6045.4
ReflectionResolution: 1.85→50 Å / Num. all: 18722 / Num. obs: 18460 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 15.6 Å2 / Rmerge(I) obs: 0.146 / Rsym value: 0.146 / Net I/σ(I): 12.5
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.703 / Mean I/σ(I) obs: 1.8 / Num. unique all: 922 / Rsym value: 0.703 / % possible all: 99.2

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.8.0049refinement
PDB_EXTRACT3.14data extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
SHELXphasing
MLPHAREphasing
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.85→48.14 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.95 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 6.185 / SU ML: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.143 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1889 949 5.1 %RANDOM
Rwork0.1483 ---
obs0.1505 18430 98.17 %-
all-18806 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 61.01 Å2 / Biso mean: 18.951 Å2 / Biso min: 8.38 Å2
Baniso -1Baniso -2Baniso -3
1-1.03 Å20 Å2-0 Å2
2---0.13 Å2-0 Å2
3----0.9 Å2
Refinement stepCycle: LAST / Resolution: 1.85→48.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1925 0 78 207 2210
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0192031
X-RAY DIFFRACTIONr_bond_other_d0.0060.022059
X-RAY DIFFRACTIONr_angle_refined_deg1.8352.0552762
X-RAY DIFFRACTIONr_angle_other_deg1.28934718
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.895260
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.8123.33372
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.00315326
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6081519
X-RAY DIFFRACTIONr_chiral_restr0.0960.2356
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022203
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02406
X-RAY DIFFRACTIONr_mcbond_it0.7160.8421034
X-RAY DIFFRACTIONr_mcbond_other0.7140.841033
X-RAY DIFFRACTIONr_mcangle_it1.1691.2561290
Refine LS restraints NCS

Ens-ID: 1 / Number: 7040 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.15 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.854→1.902 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 65 -
Rwork0.249 1190 -
all-1255 -
obs-1255 92.08 %
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)
10.5511-0.32461.20650.7629-0.24264.87250.06910.0103-0.0010.0203-0.0449-0.04660.19430.159-0.02420.0705-0.00040.01230.07330.00780.064834.042-10.94310.28
21.06041.4664-3.4452.8661-4.015612.4398-0.09810.1272-0.0157-0.16330.14740.09340.2721-0.3601-0.04930.0715-0.00380.00020.0695-0.02030.09222.43-8.106-5.762
39.1047-0.04-4.2160.3326-0.90377.5243-0.2199-0.0146-0.2003-0.02110.0228-0.1090.50440.35720.1970.10360.0420.01690.0739-0.01580.093632.808-7.397-2.496
41.7639-1.88111.09793.1603-1.33392.6176-0.02550.04420.04-0.02130.0406-0.0334-0.016-0.0822-0.01510.0464-0.00760.00380.06090.00120.056424.3244.108-4.663
52.59240.7131.55361.02260.66264.5692-0.09660.16540.0722-0.1254-0.03440.0008-0.02920.07170.1310.0883-0.00230.01240.04380.01950.065727.5251.075-10.174
64.1821-4.747710.401512.0959-18.937933.46630.10850.3546-0.104-0.2065-0.2093-0.23920.33650.71710.10080.0778-0.02070.00880.1625-0.04820.145541.191-4.6779.677
76.0345-5.45944.805610.8696-5.54695.3897-0.1759-0.11790.30790.17080.0579-0.1081-0.42150.08130.1180.0765-0.0170.00230.0562-0.01280.050535.063.31214.098
81.41030.5099-1.06391.2474-0.99543.18360.0164-0.0236-0.19080.0381-0.0617-0.0694-0.03240.18970.04530.06510.0094-0.010.0818-0.00520.090733.052-5.9749.954
92.2861-0.19251.33563.4588-0.74147.8069-0.0868-0.10850.14360.2942-0.0305-0.2041-0.18060.20460.11730.05110.00070.00360.057-0.0090.07117.6915.50420.052
105.90580.07321.10471.42520.23431.5237-0.02740.01570.0666-0.03660.02460.0078-0.0417-0.03030.00280.06710.00160.00510.05620.00260.066812.12812.1931.346
110.8216-0.8093-0.10641.12230.77851.5869-0.0060.0605-0.03820.0409-0.01260.06240.1242-0.00840.01860.05-0.02540.00720.06860.00420.08589.5683.5661.684
123.0538-0.62631.31145.4735-4.066510.91020.01170.2610.0506-0.38520.0047-0.13420.23870.2246-0.01640.0404-0.0102-0.00040.045-0.02720.0886.5284.752-4.234
131.2484-0.07050.42342.26311.81515.82240.108-0.1977-0.06470.0361-0.08710.08260.1243-0.3408-0.02090.0936-0.01530.0070.0570.02960.088511.7564.38519.767
147.8514-0.23993.916510.83551.729614.30820.0356-0.3621-0.48640.44840.0206-0.10230.3619-0.1717-0.05610.05470.00720.0250.04390.01390.102217.408-3.35117.781
156.3435-1.78190.39040.6359-0.25011.4588-0.1063-0.236-0.13230.05130.08620.03450.12190.02480.02020.0747-0.00440.00450.0657-0.00130.069413.4089.5116.025
169.6484-0.31523.666916.09180.945419.5461-0.0511-0.1173-0.16790.0432-0.1239-0.35580.41560.03130.1750.0210.0178-0.02150.1321-0.02770.089927.5468.32919.877
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A201 - 224
2X-RAY DIFFRACTION2A225 - 237
3X-RAY DIFFRACTION3A238 - 251
4X-RAY DIFFRACTION4A252 - 266
5X-RAY DIFFRACTION5A267 - 284
6X-RAY DIFFRACTION6A285 - 290
7X-RAY DIFFRACTION7A291 - 303
8X-RAY DIFFRACTION8A304 - 330
9X-RAY DIFFRACTION9B203 - 219
10X-RAY DIFFRACTION10B220 - 241
11X-RAY DIFFRACTION11B242 - 268
12X-RAY DIFFRACTION12B269 - 280
13X-RAY DIFFRACTION13B281 - 296
14X-RAY DIFFRACTION14B297 - 304
15X-RAY DIFFRACTION15B305 - 324
16X-RAY DIFFRACTION16B325 - 330

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