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Basic information

Entry
Database: PDB / ID: 3feq
TitleCrystal structure of uncharacterized protein eah89906
ComponentsPUTATIVE AMIDOHYDROLASE
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / UNKNOWN SOURCE / AMIDOHYDROLASE / SARGASSO SEA / PROTEIN STRUCTURE INITIATIVE / PSI / NEW YORK STRUCTURAL GENOMIX RESEARCH CONSORTIUM / 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 / Alpha-Beta 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
Biological speciesunidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 2.63 Å
AuthorsPatskovsky, Y. / Bonanno, J. / Romero, R. / Freeman, J. / Lau, C. / Smith, D. / Bain, K. / Wasserman, S.R. / Raushel, F. / Sauder, J.M. ...Patskovsky, Y. / Bonanno, J. / Romero, R. / Freeman, J. / Lau, C. / Smith, D. / Bain, K. / Wasserman, S.R. / Raushel, F. / Sauder, J.M. / Burley, S.K. / 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
DepositionNov 30, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2008Provider: 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 / Database references / Structure summary
Category: audit_author / struct_ref_seq
Item: _audit_author.identifier_ORCID / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end
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.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_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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)721,30948
Polymers719,21616
Non-polymers2,09332
Water2,612145
1
A: PUTATIVE AMIDOHYDROLASE
B: PUTATIVE AMIDOHYDROLASE
C: PUTATIVE AMIDOHYDROLASE
D: PUTATIVE AMIDOHYDROLASE
E: PUTATIVE AMIDOHYDROLASE
F: PUTATIVE AMIDOHYDROLASE
G: PUTATIVE AMIDOHYDROLASE
H: PUTATIVE AMIDOHYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)360,65424
Polymers359,6088
Non-polymers1,04716
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19800 Å2
ΔGint-716 kcal/mol
Surface area106380 Å2
MethodPISA
2
I: PUTATIVE AMIDOHYDROLASE
J: PUTATIVE AMIDOHYDROLASE
K: PUTATIVE AMIDOHYDROLASE
L: PUTATIVE AMIDOHYDROLASE
M: PUTATIVE AMIDOHYDROLASE
N: PUTATIVE AMIDOHYDROLASE
O: PUTATIVE AMIDOHYDROLASE
P: PUTATIVE AMIDOHYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)360,65424
Polymers359,6088
Non-polymers1,04716
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19770 Å2
ΔGint-724 kcal/mol
Surface area106480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.208, 108.048, 171.132
Angle α, β, γ (deg.)81.75, 80.36, 74.40
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91I
101J
111K
121L
131M
141N
151O
161P

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: 1 / Auth seq-ID: 2 - 409 / Label seq-ID: 4 - 411

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF
7GG
8HH
9II
10JJ
11KK
12LL
13MM
14NN
15OO
16PP
Detailshomo-octamer, the unit cell contains two octamers

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Components

#1: Protein
PUTATIVE AMIDOHYDROLASE /


Mass: 44950.988 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified (others) / 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 2.75 Å3/Da / Density % sol: 55.23 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 6% PEG 8000, MES, PH 6.0, 200MM SODIU ACYTATE,10% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9796
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 2, 2007
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.61→50 Å / Num. obs: 227280 / % possible obs: 98 % / Observed criterion σ(I): -0.5 / Redundancy: 3.1 % / Rmerge(I) obs: 0.206 / Net I/σ(I): 3.2
Reflection shellResolution: 2.61→2.7 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 1 / % possible all: 97.1

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: molecular replacement
Starting model: 2R8C

2r8c
PDB Unreleased entry


Resolution: 2.63→20 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.876 / SU B: 16.434 / SU ML: 0.327 / Cross valid method: THROUGHOUT / ESU R: 1.038 / ESU R Free: 0.362 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28148 6581 3 %RANDOM
Rwork0.23769 ---
obs0.23902 212060 96.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.115 Å2
Baniso -1Baniso -2Baniso -3
1-0.77 Å2-0.93 Å21.96 Å2
2---0.46 Å20.09 Å2
3----0.49 Å2
Refinement stepCycle: LAST / Resolution: 2.63→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms48085 0 32 145 48262
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02248967
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.081.95866451
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2356506
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.77723.8312122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.156158035
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.90515422
X-RAY DIFFRACTIONr_chiral_restr0.0880.27798
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0237092
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1960.322296
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3180.533341
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.52767
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0450.52
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3530.3160
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4940.513
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.703232452
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it7.036351207
X-RAY DIFFRACTIONr_scbond_it8.363317555
X-RAY DIFFRACTIONr_scangle_it12.458515209
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 2896 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.130.1
2Btight positional0.130.1
3Ctight positional0.140.1
4Dtight positional0.130.1
5Etight positional0.140.1
6Ftight positional0.140.1
7Gtight positional0.120.1
8Htight positional0.130.1
9Itight positional0.150.1
10Jtight positional0.130.1
11Ktight positional0.140.1
12Ltight positional0.140.1
13Mtight positional0.140.1
14Ntight positional0.130.1
15Otight positional0.120.1
16Ptight positional0.130.1
1Atight thermal5.315
2Btight thermal6.875
3Ctight thermal5.485
4Dtight thermal8.395
5Etight thermal6.255
6Ftight thermal5.785
7Gtight thermal5.045
8Htight thermal7.785
9Itight thermal7.045
10Jtight thermal7.775
11Ktight thermal7.345
12Ltight thermal8.035
13Mtight thermal7.215
14Ntight thermal6.375
15Otight thermal4.185
16Ptight thermal4.765
LS refinement shellResolution: 2.631→2.698 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.44 440 -
Rwork0.414 13514 -
obs--84.54 %

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