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- PDB-3n2c: Crystal structure of prolidase eah89906 complexed with n-methylph... -

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Basic information

Entry
Database: PDB / ID: 3n2c
TitleCrystal structure of prolidase eah89906 complexed with n-methylphosphonate-l-proline
ComponentsPROLIDASE
KeywordsHYDROLASE / UNKNOWN SOURCE / AMIDOHYDROLASE / SARGASSO SEA / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / PSI / NEW YORK STRUCTURAL GENOMIX RESEARCH CONSORTIUM / PROLIDASE / NYSGXRC / NEW YORK SGX RESEARCH CENTER FOR STRUCTURAL GENOMICS
Function / homology
Function and homology information


hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / metal ion binding / cytoplasm
Similarity search - Function
: / Urease, subunit C; domain 1 / Urease, subunit C, domain 1 / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolases / Metal-dependent hydrolase / Roll / TIM Barrel ...: / Urease, subunit C; domain 1 / Urease, subunit C, domain 1 / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolases / Metal-dependent hydrolase / Roll / TIM Barrel / Alpha-Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
1-[(R)-hydroxy(methyl)phosphoryl]-L-proline / Amidohydrolase
Similarity search - Component
Biological speciesUNIDENTIFIED (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 2.81 Å
AuthorsPatskovsky, Y. / Xu, C. / Sauder, J.M. / Burley, S.K. / Raushel, F.M. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: Biochemistry / Year: 2010
Title: Functional identification and structure determination of two novel prolidases from cog1228 in the amidohydrolase superfamily .
Authors: Xiang, D.F. / Patskovsky, Y. / Xu, C. / Fedorov, A.A. / Fedorov, E.V. / Sisco, A.A. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / Raushel, F.M.
History
DepositionMay 17, 2010Deposition site: RCSB / Processing site: RCSB
SupersessionJun 2, 2010ID: 3LWY
Revision 1.0Jun 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 10, 2012Group: Database references
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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Sep 6, 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
Revision 1.6Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROLIDASE
B: PROLIDASE
C: PROLIDASE
D: PROLIDASE
E: PROLIDASE
F: PROLIDASE
G: PROLIDASE
H: PROLIDASE
I: PROLIDASE
J: PROLIDASE
K: PROLIDASE
L: PROLIDASE
M: PROLIDASE
N: PROLIDASE
O: PROLIDASE
P: PROLIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)725,08764
Polymers719,90416
Non-polymers5,18348
Water00
1
A: PROLIDASE
B: PROLIDASE
C: PROLIDASE
D: PROLIDASE
E: PROLIDASE
F: PROLIDASE
G: PROLIDASE
H: PROLIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)362,54432
Polymers359,9528
Non-polymers2,59224
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19950 Å2
ΔGint-112 kcal/mol
Surface area104660 Å2
MethodPISA
2
I: PROLIDASE
J: PROLIDASE
K: PROLIDASE
L: PROLIDASE
M: PROLIDASE
N: PROLIDASE
O: PROLIDASE
P: PROLIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)362,54432
Polymers359,9528
Non-polymers2,59224
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20290 Å2
ΔGint-115 kcal/mol
Surface area104490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.186, 108.035, 170.772
Angle α, β, γ (deg.)81.32, 80.47, 73.76
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
PROLIDASE


Mass: 44993.988 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) UNIDENTIFIED (others) / Production host: Escherichia coli (E. coli) / References: UniProt: Q393A1*PLUS
#2: Chemical...
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 32 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-LWY / 1-[(R)-hydroxy(methyl)phosphoryl]-L-proline


Type: L-peptide NH3 amino terminus / Mass: 193.138 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C6H12NO4P

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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: 2.74 Å3/Da / Density % sol: 55.19 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 6
Details: 8% PEG8000, MES, PH 6.0, 200MM SODIUM ACETATE, 10% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 280K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 18, 2009 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 186340 / % possible obs: 98.3 % / Observed criterion σ(I): -5 / Redundancy: 1.9 % / Biso Wilson estimate: 76.32 Å2 / Rmerge(I) obs: 0.18 / Net I/σ(I): 3.5
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 0.5 / % possible all: 97

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: molecular replacement
Starting model: PDB ENTRY 3FEQ

3feq


Resolution: 2.81→40 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.906 / SU B: 21.786 / SU ML: 0.396 / Cross valid method: THROUGHOUT / ESU R Free: 0.439 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27297 5054 3 %RANDOM
Rwork0.22023 ---
obs0.22182 162394 89.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 85.979 Å2
Baniso -1Baniso -2Baniso -3
1-0.38 Å2-1.23 Å22.2 Å2
2--0.38 Å2-0.01 Å2
3----0.8 Å2
Refinement stepCycle: LAST / Resolution: 2.81→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms48528 0 224 0 48752
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02249424
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1421.96567072
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.55156512
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.29923.9552144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.639158048
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.00815416
X-RAY DIFFRACTIONr_chiral_restr0.0770.27840
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02137488
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_it3.008232288
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.326351680
X-RAY DIFFRACTIONr_scbond_it7.757417136
X-RAY DIFFRACTIONr_scangle_it12.096615392
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.806→2.879 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 163 -
Rwork0.354 5458 -
obs--40.91 %

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