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- PDB-3qvk: Allantoin racemase from Klebsiella pneumoniae -

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Basic information

Entry
Database: PDB / ID: 3qvk
TitleAllantoin racemase from Klebsiella pneumoniae
ComponentsPutative hydantoin racemase
KeywordsISOMERASE / Allantoin Racemase
Function / homology
Function and homology information


hydantoin racemase / amino-acid racemase activity
Similarity search - Function
: / Rossmann fold - #12500 / : / Asp/Glu/hydantoin racemase / Asp/Glu/Hydantoin racemase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
1-(2,5-DIOXO-2,5-DIHYDRO-1H-IMIDAZOL-4-YL)UREA / Hydantoin racemase
Similarity search - Component
Biological speciesKlebsiella pneumoniae subsp. pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.999 Å
AuthorsFrench, J.B. / Neau, D.B. / Ealick, S.E.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Characterization of the Structure and Function of Klebsiella pneumoniae Allantoin Racemase.
Authors: French, J.B. / Neau, D.B. / Ealick, S.E.
History
DepositionFeb 25, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Putative hydantoin racemase
B: Putative hydantoin racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4474
Polymers51,1352
Non-polymers3122
Water5,260292
1
A: Putative hydantoin racemase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)154,34212
Polymers153,4056
Non-polymers9376
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation10_664-y+1,-x+1,-z-1/21
crystal symmetry operation11_654-x+y+1,y,-z-1/21
crystal symmetry operation12_554x,x-y,-z-1/21
Buried area23970 Å2
ΔGint-135 kcal/mol
Surface area44160 Å2
MethodPISA
2
B: Putative hydantoin racemase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)154,34212
Polymers153,4056
Non-polymers9376
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_555x-y,-y,-z1
crystal symmetry operation9_555-x,-x+y,-z1
Buried area24470 Å2
ΔGint-140 kcal/mol
Surface area43110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.896, 124.896, 126.972
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-251-

HOH

21A-294-

HOH

31A-365-

HOH

41B-292-

HOH

51B-298-

HOH

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Components

#1: Protein Putative hydantoin racemase


Mass: 25567.549 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae (bacteria)
Strain: ATCC 700721 / MGH 78578 / Gene: HpxA, KPN78578_17580, KPN_01788 / Production host: Escherichia coli (E. coli) / References: UniProt: A6T9E8
#2: Chemical ChemComp-2AL / 1-(2,5-DIOXO-2,5-DIHYDRO-1H-IMIDAZOL-4-YL)UREA / ALLANTOIN


Mass: 156.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H4N4O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 292 / Source method: isolated from a natural source / Formula: H2O

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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: 2.8 Å3/Da / Density % sol: 56 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 3.9
Details: 30% Peg 400, 0.1 M sodium acetate pH 3.9, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 5, 2009
RadiationMonochromator: CRYO-COOLED SI(111) DOUBLECRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.999→108.163 Å / Num. all: 39452 / Num. obs: 39452 / % possible obs: 98.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5 % / Rmerge(I) obs: 0.096 / Χ2: 2.498 / Net I/σ(I): 13.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.999-2.074.50.38138661.599198.2
2.07-2.155.20.28238731.832198.4
2.15-2.255.20.22738872.119198.6
2.25-2.375.20.18538922.376198.7
2.37-2.525.10.15139032.547198.8
2.52-2.715.10.12439372.982198.8
2.71-2.995.10.11639582.786199
2.99-3.425.10.10239893.041199.1
3.42-4.3150.09540373.554198.9
4.31-504.80.05941101.982195.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
SOLVEphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.999→108.16 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.933 / Occupancy max: 1 / Occupancy min: 0.45 / SU B: 4.029 / SU ML: 0.113 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.191 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2456 1974 5 %RANDOM
Rwork0.2208 ---
all0.222 39452 --
obs0.222 39437 98.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 62.83 Å2 / Biso mean: 31.954 Å2 / Biso min: 19.73 Å2
Baniso -1Baniso -2Baniso -3
1--0.71 Å2-0.36 Å20 Å2
2---0.71 Å20 Å2
3---1.07 Å2
Refinement stepCycle: LAST / Resolution: 1.999→108.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3534 0 22 292 3848
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0223651
X-RAY DIFFRACTIONr_angle_refined_deg0.9271.9794965
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.435494
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.18223.846130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.915579
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5911523
X-RAY DIFFRACTIONr_chiral_restr0.0520.2597
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0212732
X-RAY DIFFRACTIONr_mcbond_it0.1951.52440
X-RAY DIFFRACTIONr_mcangle_it0.36723882
X-RAY DIFFRACTIONr_scbond_it0.45231211
X-RAY DIFFRACTIONr_scangle_it0.8144.51083
LS refinement shellResolution: 1.999→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 152 -
Rwork0.266 2718 -
all-2870 -
obs--98.22 %

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