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- PDB-3be7: Crystal structure of Zn-dependent arginine carboxypeptidase -

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Basic information

Entry
Database: PDB / ID: 3be7
TitleCrystal structure of Zn-dependent arginine carboxypeptidase
ComponentsZn-dependent arginine carboxypeptidase
KeywordsHYDROLASE / UNKNOWN SOURCE / AMIDOHYDROLASE / SARGASSO SEA / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / PSI / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homologyUrease, subunit C; domain 1 / Urease, subunit C, domain 1 / Metal-dependent hydrolases / Roll / TIM Barrel / Alpha-Beta Barrel / Mainly Beta / Alpha Beta / ARGININE
Function and homology information
Biological speciesunidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsPatskovsky, Y. / Ramagopal, U.A. / Toro, R. / Meyer, A.J. / Freeman, J. / Iizuka, M. / Bain, K. / Rodgers, L. / Raushel, F. / Sauder, J.M. ...Patskovsky, Y. / Ramagopal, U.A. / Toro, R. / Meyer, A.J. / Freeman, J. / Iizuka, M. / Bain, K. / Rodgers, L. / Raushel, F. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: Biochemistry / Year: 2009
Title: Functional identification of incorrectly annotated prolidases from the amidohydrolase superfamily of enzymes.
Authors: Xiang, D.F. / Patskovsky, Y. / Xu, C. / Meyer, A.J. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / Raushel, F.M.
History
DepositionNov 16, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.3Feb 3, 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_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Zn-dependent arginine carboxypeptidase
B: Zn-dependent arginine carboxypeptidase
C: Zn-dependent arginine carboxypeptidase
D: Zn-dependent arginine carboxypeptidase
E: Zn-dependent arginine carboxypeptidase
F: Zn-dependent arginine carboxypeptidase
G: Zn-dependent arginine carboxypeptidase
H: Zn-dependent arginine carboxypeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)358,47234
Polymers355,5488
Non-polymers2,92426
Water10,305572
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.420, 146.583, 255.963
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain: (Details: A B C D E F G H)

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Components

#1: Protein
Zn-dependent arginine carboxypeptidase


Mass: 44443.520 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified (others) / Description: Environmental sample from Sargasso Sea / Gene: IBEA_CTG=2118574 / Plasmid: pSGX3(BC) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
#2: Chemical
ChemComp-ARG / ARGININE / Arginine


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H15N4O2
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 572 / 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: 2.98 Å3/Da / Density % sol: 58.73 %
Crystal growTemperature: 294 K / pH: 7
Details: 100mM Succinic acid pH 7.0, 15% PEG 3350, 10% Glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 8, 2007 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 230541 / % possible obs: 94.8 % / Observed criterion σ(I): -0.5 / Redundancy: 4.2 % / Biso Wilson estimate: 20.2 Å2 / Rmerge(I) obs: 0.13 / Rsym value: 0.1 / Net I/σ(I): 3.7
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 0.8 / Rsym value: 0.54 / % possible all: 87.4

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.3.0034refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2R8C

2r8c
PDB Unreleased entry


Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.902 / SU B: 10.401 / SU ML: 0.24 / Cross valid method: THROUGHOUT / ESU R: 0.305 / ESU R Free: 0.248 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27981 5451 3 %RANDOM
Rwork0.22602 ---
obs0.22767 175832 95.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.347 Å2
Baniso -1Baniso -2Baniso -3
1--1.44 Å20 Å20 Å2
2--1.48 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24048 0 194 572 24814
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02224771
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.051.95333400
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.96853198
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.4624.8521082
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.232154456
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.08115134
X-RAY DIFFRACTIONr_chiral_restr0.1040.23784
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0218392
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1270.311599
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.290.516570
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.51845
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0890.326
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1060.54
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.1891.516092
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it7.128225160
X-RAY DIFFRACTIONr_scbond_it10.0239587
X-RAY DIFFRACTIONr_scangle_it13.4854.58218
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 2866 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Atight positional0.40.1
Btight positional0.380
Ctight positional0.360
Dtight positional0.360
Etight positional0.390
Ftight positional0.410
Gtight positional0.480
Htight positional0.440
Atight thermal5.311.5
Btight thermal5.240
Ctight thermal5.290
Dtight thermal4.780
Etight thermal5.580
Ftight thermal5.680
Gtight thermal4.810
Htight thermal7.120
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.404 385 -
Rwork0.337 12093 -
obs--90.91 %

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