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- PDB-2eq5: Crystal structure of hydantoin racemase from Pyrococcus horikoshii OT3 -

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Basic information

Entry
Database: PDB / ID: 2eq5
TitleCrystal structure of hydantoin racemase from Pyrococcus horikoshii OT3
Components228aa long hypothetical hydantoin racemase
KeywordsISOMERASE / racemase / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homologyracemase activity, acting on amino acids and derivatives / Rossmann fold - #1860 / Asp/Glu/hydantoin racemase / Asp/Glu/Hydantoin racemase / : / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / 228aa long hypothetical hydantoin racemase
Function and homology information
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsMizutani, H. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of hydantoin racemase from Pyrococcus horikoshii OT3
Authors: Mizutani, H. / Kunishima, N.
History
DepositionMar 30, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: 228aa long hypothetical hydantoin racemase
B: 228aa long hypothetical hydantoin racemase
C: 228aa long hypothetical hydantoin racemase
D: 228aa long hypothetical hydantoin racemase


Theoretical massNumber of molelcules
Total (without water)100,0764
Polymers100,0764
Non-polymers00
Water8,017445
1
A: 228aa long hypothetical hydantoin racemase
B: 228aa long hypothetical hydantoin racemase


Theoretical massNumber of molelcules
Total (without water)50,0382
Polymers50,0382
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: 228aa long hypothetical hydantoin racemase
D: 228aa long hypothetical hydantoin racemase


Theoretical massNumber of molelcules
Total (without water)50,0382
Polymers50,0382
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)152.707, 152.707, 81.257
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein
228aa long hypothetical hydantoin racemase


Mass: 25019.084 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL
References: UniProt: O58781, Isomerases; Racemases and epimerases
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 445 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.73 Å3/Da / Density % sol: 54.97 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 4.1
Details: 11.25% (w/v) PEG 8000, 0.5M Li2SO4, pH 4.1, microbatch, temperature 295K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU11.5418
SYNCHROTRONSPring-8 BL26B120.979056
Detector
TypeIDDetectorDate
RIGAKU RAXIS VII1IMAGE PLATENov 4, 2004
RIGAKU JUPITER 2102CCDDec 14, 2006
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1mirrorsSINGLE WAVELENGTHMx-ray1
2bending magnetSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
20.9790561
ReflectionResolution: 2.2→30 Å / Num. all: 54955 / Num. obs: 54955 / % possible obs: 99.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 7.5 % / Biso Wilson estimate: 29.6 Å2 / Rmerge(I) obs: 0.073 / Rsym value: 0.062 / Net I/σ(I): 13.9
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.413 / Mean I/σ(I) obs: 5.29 / Rsym value: 0.376 / % possible all: 99

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→30 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2515254.88 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: THIS IS A TWINNED STRUCTURE. THE TWINNING OPERATOR IS (H,K,L) -> (H,-H-K,-L) AND THE TWINNING FRACTION IS 0.334
RfactorNum. reflection% reflectionSelection details
Rfree0.222 2540 4.6 %RANDOM
Rwork0.16 ---
all0.163 54807 --
obs0.16 54807 99.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 57.3742 Å2 / ksol: 0.34777 e/Å3
Displacement parametersBiso mean: 43 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å24.26 Å20 Å2
2---0.07 Å20 Å2
3---0.14 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.42 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6416 0 0 445 6861
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.261.5
X-RAY DIFFRACTIONc_mcangle_it2.152
X-RAY DIFFRACTIONc_scbond_it1.892
X-RAY DIFFRACTIONc_scangle_it2.952.5
LS refinement shellResolution: 2.2→2.3 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.293 300 4.6 %
Rwork0.258 6537 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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