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

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Basic information

Entry
Database: PDB / ID: 3qvj
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
Biological speciesKlebsiella pneumoniae subsp. pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 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 1.3Nov 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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

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Assembly

Deposited unit
A: Putative hydantoin racemase
B: Putative hydantoin racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8334
Polymers51,7622
Non-polymers712
Water3,153175
1
A: Putative hydantoin racemase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)155,49912
Polymers155,2866
Non-polymers2136
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 area23150 Å2
ΔGint-219 kcal/mol
Surface area43050 Å2
MethodPISA
2
B: Putative hydantoin racemase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)155,49912
Polymers155,2866
Non-polymers2136
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 area22470 Å2
ΔGint-204 kcal/mol
Surface area43710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.819, 124.819, 126.840
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-264-

HOH

21B-265-

HOH

31B-294-

HOH

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Components

#1: Protein Putative hydantoin racemase


Mass: 25881.049 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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 2.76 Å3/Da / Density % sol: 55.36 %
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-C / Wavelength: 0.9792 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: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 34597 / Num. obs: 34504 / % possible obs: 94.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.097 / Χ2: 1.547 / Net I/σ(I): 7.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.1-2.243.50.40114710.466199.6
2.24-2.283.60.35814840.459199.9
2.28-2.323.60.31714530.464199.2
2.32-2.373.70.28114640.478199.3
2.37-2.423.60.26114690.481199.2
2.42-2.483.70.24414580.541198.9
2.48-2.543.70.19814790.543198.2
2.54-2.613.70.1814410.6197.8
2.61-2.693.70.15514470.619197.7
2.69-2.773.70.13814520.729196.9
2.77-2.873.70.12414440.817196.6
2.87-2.993.70.11714201.011195.4
2.99-3.123.80.09914301.186194.6
3.12-3.293.80.09714201.626194.2
3.29-3.493.80.08514022.268193
3.49-3.763.80.08213872.743191.5
3.76-4.143.80.09413833.45190.3
4.14-4.743.90.08513623.511188.3
4.74-5.973.90.0713324.04184.6
5.97-5040.05513634.655180.1

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEphasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: SAD / Resolution: 2.1→35 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.937 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 4.372 / SU ML: 0.117 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.198 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2388 1740 5 %RANDOM
Rwork0.2029 ---
all0.2047 32765 --
obs0.2047 32765 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 59.09 Å2 / Biso mean: 33.4297 Å2 / Biso min: 19.64 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20.01 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.1→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3527 0 2 175 3704
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0223597
X-RAY DIFFRACTIONr_angle_refined_deg1.0111.9714892
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0325492
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.77123.566129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.68415572
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2691525
X-RAY DIFFRACTIONr_chiral_restr0.0690.2596
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212677
X-RAY DIFFRACTIONr_mcbond_it0.3851.52429
X-RAY DIFFRACTIONr_mcangle_it0.77223865
X-RAY DIFFRACTIONr_scbond_it1.58331168
X-RAY DIFFRACTIONr_scangle_it2.664.51025
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 128 -
Rwork0.259 2366 -
all-2494 -
obs--99.44 %

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