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- PDB-3icj: Crystal structure of an uncharacterized metal-dependent hydrolase... -

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Basic information

Entry
Database: PDB / ID: 3icj
TitleCrystal structure of an uncharacterized metal-dependent hydrolase from pyrococcus furiosus
Componentsuncharacterized metal-dependent hydrolase
KeywordsHYDROLASE / STRUCTURAL GENOMICS / AMIDOHYDROLASE / PSI-2 / PROTEIN STRUCTURE INITIATIVE / NEW YORK SGX RESEARCH CENTER FOR STRUCTURAL GENOMICS / NYSGXRC
Function / homology
Function and homology information


hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / metal ion binding
Similarity search - Function
Diaminopimelate Epimerase; Chain A, domain 1 - #70 / YtcJ like / TatD deoxyribonuclease family signature 1. / Deoxyribonuclease, TatD-related, conserved site / Amidohydrolase 3 / Amidohydrolase family / Diaminopimelate Epimerase; Chain A, domain 1 / Urease, subunit C; domain 1 / Urease, subunit C, domain 1 / Metal-dependent hydrolase, composite domain superfamily ...Diaminopimelate Epimerase; Chain A, domain 1 - #70 / YtcJ like / TatD deoxyribonuclease family signature 1. / Deoxyribonuclease, TatD-related, conserved site / Amidohydrolase 3 / Amidohydrolase family / Diaminopimelate Epimerase; Chain A, domain 1 / Urease, subunit C; domain 1 / Urease, subunit C, domain 1 / Metal-dependent hydrolase, composite domain superfamily / Metal-dependent hydrolases / Metal-dependent hydrolase / Roll / TIM Barrel / Roll / Alpha-Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Amidohydrolase 3 domain-containing protein
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsBonanno, J.B. / Patskovsky, Y. / Freeman, J. / Bain, K.T. / Hu, S. / Ozyurt, S. / Wasserman, S. / Sauder, J.M. / Raushel, F.M. / Burley, S.K. ...Bonanno, J.B. / Patskovsky, Y. / Freeman, J. / Bain, K.T. / Hu, S. / Ozyurt, S. / Wasserman, S. / Sauder, J.M. / Raushel, F.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal Structure of an Uncharacterized Metal-Dependent Hydrolase from Pyrococcus Furiosus
Authors: Bonanno, J.B. / Patskovsky, Y. / Freeman, J. / Bain, K.T. / Hu, S. / Ozyurt, S. / Wasserman, S. / Sauder, J.M. / Raushel, F.M. / Burley, S.K. / Almo, S.C.
History
DepositionJul 17, 2009Deposition site: RCSB / Processing site: RCSB
SupersessionJul 28, 2009ID: 3ETK
Revision 1.0Jul 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.3Nov 21, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _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: uncharacterized metal-dependent hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,5143
Polymers60,3831
Non-polymers1312
Water5,116284
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.869, 116.438, 169.660
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein uncharacterized metal-dependent hydrolase


Mass: 60383.102 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: PF0846 / Plasmid: MODIFIED PET26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8U2I8
#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.: 284 / 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: 2.41 Å3/Da / Density % sol: 48.94 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 7
Details: 20% PEG 3350, 200MM MAGNESIUM FORMATE, 10% GLYCEROL, PH 7.0, VAPOR DIFFUSION, TEMPERATURE 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97958
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 3, 2008
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97958 Å / Relative weight: 1
ReflectionResolution: 1.95→38.5 Å / Num. obs: 42947 / % possible obs: 96.6 % / Observed criterion σ(I): 0 / Redundancy: 12.5 % / Biso Wilson estimate: 34.789 Å2 / Rmerge(I) obs: 0.097 / Rsym value: 0.097 / Net I/σ(I): 12.4
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 13 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2.4 / Rsym value: 0.65 / % possible all: 94

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Processing

Software
NameVersionClassification
SHELXCDphasing
SHELXEmodel building
REFMAC5.5.0089refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.95→20 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.937 / SU B: 10.613 / SU ML: 0.129 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.171 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26718 1286 3.1 %RANDOM
Rwork0.20722 ---
obs0.20903 40027 96.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 41.14 Å2
Baniso -1Baniso -2Baniso -3
1-2.78 Å20 Å20 Å2
2--0.7 Å20 Å2
3----3.48 Å2
Refinement stepCycle: LAST / Resolution: 1.95→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3730 0 2 284 4016
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223871
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3191.9765237
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5675489
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.27923.481181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.44915728
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1481535
X-RAY DIFFRACTIONr_chiral_restr0.0870.2585
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212901
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.08822357
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.24833810
X-RAY DIFFRACTIONr_scbond_it6.0231514
X-RAY DIFFRACTIONr_scangle_it8.48751415
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.615 91 -
Rwork0.522 2796 -
obs--92.77 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.66251.7885-0.66784.7058-2.04313.60090.0642-0.0113-0.22290.0575-0.09550.06520.1931-0.1840.03130.0694-0.01680.00040.0356-0.02490.13741.6822-19.187929.1347
23.63620.40392.18144.7702-1.40788.45330.23980.1002-0.1521-0.1701-0.0878-0.01410.5362-0.1376-0.1520.14750.0382-0.01250.11880.02860.1025-9.959923.6058.5856
30.83670.0193-0.60780.55710.02811.26110.0120.04770.01760.0051-0.0022-0.0385-0.07070.0404-0.00990.0253-0.014-0.02390.02540.01090.043210.82917.886621.6655
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A34 - 94
2X-RAY DIFFRACTION1A480 - 501
3X-RAY DIFFRACTION2A110 - 213
4X-RAY DIFFRACTION3A95 - 109
5X-RAY DIFFRACTION3A214 - 479

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