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- PDB-3hpa: Crystal structure of an amidohydrolase gi:44264246 from an eviron... -

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Basic information

Entry
Database: PDB / ID: 3hpa
TitleCrystal structure of an amidohydrolase gi:44264246 from an evironmental sample of sargasso sea
ComponentsAMIDOHYDROLASE
KeywordsHYDROLASE / AMIDOHYDROLASE / SIGNATURE OF ZN LIGANDS / STRUCTURAL GENOMICS / NYSGXRC / TARGET 9236E / PSI-2 / PROTEIN STRUCTURE INITIATIVE / NEW YORK SGX RESEARCH CENTER FOR STRUCTURAL GENOMICS
Function / homologyUrease, subunit C; domain 1 / Urease, subunit C, domain 1 / Metal-dependent hydrolases / Roll / TIM Barrel / Alpha-Beta Barrel / Mainly Beta / Alpha Beta
Function and homology information
Biological speciesunidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsFedorov, A.A. / Fedorov, E.V. / Toro, R. / Raushel, F.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: J.Am.Chem.Soc. / Year: 2010
Title: The hunt for 8-oxoguanine deaminase.
Authors: Hall, R.S. / Fedorov, A.A. / Marti-Arbona, R. / Fedorov, E.V. / Kolb, P. / Sauder, J.M. / Burley, S.K. / Shoichet, B.K. / Almo, S.C. / Raushel, F.M.
History
DepositionJun 3, 2009Deposition site: RCSB / Processing site: RCSB
SupersessionJun 16, 2009ID: 3H4U
Revision 1.0Jun 16, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 21, 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: AMIDOHYDROLASE
B: AMIDOHYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,8024
Polymers103,6722
Non-polymers1312
Water2,324129
1
A: AMIDOHYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9012
Polymers51,8361
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: AMIDOHYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9012
Polymers51,8361
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4580 Å2
ΔGint-104 kcal/mol
Surface area27770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.304, 83.304, 229.125
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-503-

HOH

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Components

#1: Protein AMIDOHYDROLASE


Mass: 51835.836 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: EVIRONMENTAL SAMPLE OF SARGASSO SEA / Source: (gene. exp.) unidentified (others) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 2.21 Å3/Da / Density % sol: 44.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.8M SODIUM ACETATE, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 15, 2008
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.2→25 Å / Num. all: 47567 / Num. obs: 47567 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 27.9 Å2 / Rmerge(I) obs: 0.079

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
BALBESphasing
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→24.62 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2073974.63 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.276 2406 5.1 %RANDOM
Rwork0.232 ---
all0.233 47567 --
obs0.232 47567 99.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 62.4521 Å2 / ksol: 0.39385 e/Å3
Displacement parametersBiso mean: 43.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å21.08 Å20 Å2
2---0.02 Å20 Å2
3---0.04 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.2→24.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6494 0 2 129 6625
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_mcbond_it1.21.5
X-RAY DIFFRACTIONc_mcangle_it1.82
X-RAY DIFFRACTIONc_scbond_it2.072
X-RAY DIFFRACTIONc_scangle_it2.872.5
LS refinement shellResolution: 2.2→2.28 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.325 243 5.4 %
Rwork0.301 4288 -
obs-4288 97 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4cis_peptide.param&_1_TOPOLOGY_INFILE_4
X-RAY DIFFRACTION5&_1_PARAMETER_INFILE_5&_1_TOPOLOGY_INFILE_5

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