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- PDB-9k2p: The crystal structure of CapA1 from Capnocytophaga ochracea -

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Basic information

Entry
Database: PDB / ID: 9k2p
TitleThe crystal structure of CapA1 from Capnocytophaga ochracea
ComponentsPyridoxal-5'-phosphate-dependent protein beta subunit
KeywordsBIOSYNTHETIC PROTEIN / PLP-dependent enzyme
Function / homologycysteate synthase / alpha-amino acid metabolic process / : / Pyridoxal-phosphate dependent enzyme / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Cysteate synthase
Function and homology information
Biological speciesCapnocytophaga ochracea DSM 7271 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å
AuthorsZhang, L. / Yang, S. / Zhang, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: The crystal structure of CapA1 from Capnocytophaga ochracea
Authors: Yang, S. / Zhang, Y.
History
DepositionOct 17, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 22, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pyridoxal-5'-phosphate-dependent protein beta subunit
B: Pyridoxal-5'-phosphate-dependent protein beta subunit


Theoretical massNumber of molelcules
Total (without water)74,1622
Polymers74,1622
Non-polymers00
Water11,241624
1
A: Pyridoxal-5'-phosphate-dependent protein beta subunit

A: Pyridoxal-5'-phosphate-dependent protein beta subunit


Theoretical massNumber of molelcules
Total (without water)74,1622
Polymers74,1622
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area4600 Å2
ΔGint-27 kcal/mol
Surface area23530 Å2
MethodPISA
2
B: Pyridoxal-5'-phosphate-dependent protein beta subunit

B: Pyridoxal-5'-phosphate-dependent protein beta subunit


Theoretical massNumber of molelcules
Total (without water)74,1622
Polymers74,1622
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area4480 Å2
ΔGint-26 kcal/mol
Surface area24080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.830, 107.110, 122.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221
Components on special symmetry positions
IDModelComponents
11A-405-

HOH

21B-705-

HOH

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Components

#1: Protein Pyridoxal-5'-phosphate-dependent protein beta subunit


Mass: 37080.992 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Capnocytophaga ochracea DSM 7271 (bacteria)
Gene: Coch_1829 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C7M8J5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 624 / Source method: isolated from a natural source / Formula: H2O
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: 4 Å3/Da / Density % sol: 69.27 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: magenesium acetate tetrahydrate, MOPS, PEG8000

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Data collection

DiffractionMean temperature: 291.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 27, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.08→30.8159 Å / Num. obs: 72122 / % possible obs: 99.91 % / Redundancy: 7.9 % / CC1/2: 0.863 / Net I/σ(I): 8.7
Reflection shellResolution: 2.08→2.154 Å / Num. unique obs: 138137 / CC1/2: 0.75

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Processing

Software
NameVersionClassification
PHENIX(1.14_3247: ???)refinement
xia2data reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.08→28.922 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 22.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2077 1935 2.77 %
Rwork0.18 --
obs0.1808 69815 96.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.08→28.922 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5218 0 0 624 5842
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075326
X-RAY DIFFRACTIONf_angle_d0.8847202
X-RAY DIFFRACTIONf_dihedral_angle_d5.5473200
X-RAY DIFFRACTIONf_chiral_restr0.055792
X-RAY DIFFRACTIONf_plane_restr0.006932
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.08-2.1320.32921340.29374539X-RAY DIFFRACTION92
2.132-2.18960.34161310.27024636X-RAY DIFFRACTION93
2.1896-2.2540.3031330.26534541X-RAY DIFFRACTION92
2.254-2.32680.29151300.23124677X-RAY DIFFRACTION94
2.3268-2.40990.23611330.21524731X-RAY DIFFRACTION96
2.4099-2.50630.2421380.19324775X-RAY DIFFRACTION96
2.5063-2.62030.22361370.1894849X-RAY DIFFRACTION97
2.6203-2.75840.2111370.19034872X-RAY DIFFRACTION98
2.7584-2.9310.2551390.19254940X-RAY DIFFRACTION99
2.931-3.15710.23581430.18934940X-RAY DIFFRACTION99
3.1571-3.47430.21661420.17724994X-RAY DIFFRACTION100
3.4743-3.9760.17651430.1565046X-RAY DIFFRACTION100
3.976-5.00510.15591450.14265072X-RAY DIFFRACTION100
5.0051-28.9210.1861500.17165268X-RAY DIFFRACTION99

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