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- PDB-3mkc: Crystal structure of a putative racemase -

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Basic information

Entry
Database: PDB / ID: 3mkc
TitleCrystal structure of a putative racemase
Componentsracemase
KeywordsISOMERASE / Metabolic Process / Madalate racemase / PSI2 / NYSGXRC / Structural Genomics / Protein Structure Initiative / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


catalytic activity / metal ion binding
Similarity search - Function
Mandelate racemase DgoD-like / Mandelate racemase/muconate lactonizing enzyme, N-terminal domain / Mandelate racemase / muconate lactonizing enzyme, N-terminal domain / Enolase C-terminal domain-like / Enolase C-terminal domain-like / Enolase-like C-terminal domain / Enolase-like, N-terminal domain / Enolase-like, N-terminal / Enolase-like, C-terminal domain superfamily / Enolase-like; domain 1 ...Mandelate racemase DgoD-like / Mandelate racemase/muconate lactonizing enzyme, N-terminal domain / Mandelate racemase / muconate lactonizing enzyme, N-terminal domain / Enolase C-terminal domain-like / Enolase C-terminal domain-like / Enolase-like C-terminal domain / Enolase-like, N-terminal domain / Enolase-like, N-terminal / Enolase-like, C-terminal domain superfamily / Enolase-like; domain 1 / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesPseudovibrio sp. JE062 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.77 Å
AuthorsEswaramoorthy, S. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of a putative racemase
Authors: Eswaramoorthy, S. / Burley, S.K. / Swaminathan, S.
History
DepositionApr 14, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author / struct_conn
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: racemase


Theoretical massNumber of molelcules
Total (without water)44,4421
Polymers44,4421
Non-polymers00
Water2,738152
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: racemase
x 8


Theoretical massNumber of molelcules
Total (without water)355,5348
Polymers355,5348
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
crystal symmetry operation5_655-x+1,y,-z1
crystal symmetry operation6_565x,-y+1,-z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_665-y+1,-x+1,-z1
Buried area29530 Å2
ΔGint-48 kcal/mol
Surface area97920 Å2
MethodPISA
3
A: racemase

A: racemase


Theoretical massNumber of molelcules
Total (without water)88,8832
Polymers88,8832
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_565x,-y+1,-z1
Buried area3330 Å2
ΔGint-13 kcal/mol
Surface area28530 Å2
MethodPISA
4
A: racemase

A: racemase


Theoretical massNumber of molelcules
Total (without water)88,8832
Polymers88,8832
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area2480 Å2
ΔGint-7 kcal/mol
Surface area29380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.838, 134.838, 94.323
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-395-

HOH

21A-396-

HOH

31A-499-

HOH

41A-540-

HOH

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Components

#1: Protein racemase


Mass: 44441.699 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudovibrio sp. JE062 (bacteria) / Gene: PJE062_745 / Plasmid: BC - pSGX3 (BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Codon+RIL / References: UniProt: B6R2Z6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.41 Å3/Da / Density % sol: 49 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 2M Ammonium Sulfate; 0.1M Bis-Tris pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9788 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 7, 2010 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 1.77→50 Å / Num. all: 42424 / Num. obs: 42424 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 29 % / Biso Wilson estimate: 19.2 Å2 / Rmerge(I) obs: 0.083 / Rsym value: 0.083 / Net I/σ(I): 15.9
Reflection shellResolution: 1.77→1.82 Å / Redundancy: 25.8 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 8.9 / Num. unique all: 3477 / Rsym value: 0.45 / % possible all: 100

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Processing

Software
NameVersionClassification
CBASSdata collection
SHELXmodel building
SHARPphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.77→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.241 1612 -RANDOM
Rwork0.216 ---
all0.237 40312 --
obs0.237 40312 95 %-
Displacement parametersBiso mean: 20.4 Å2
Baniso -1Baniso -2Baniso -3
1--1.92 Å20 Å20 Å2
2---1.92 Å20 Å2
3---3.83 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.77→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2963 0 0 152 3115
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_deg22.5
X-RAY DIFFRACTIONc_improper_angle_deg0.87
LS refinement shellResolution: 1.77→1.88 Å / Rfactor Rfree error: 0.018
RfactorNum. reflection% reflection
Rfree0.285 241 -
Rwork0.255 --
obs-6270 89.9 %

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