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- PDB-4qr8: Crystal Structure of E coli pepQ -

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Basic information

Entry
Database: PDB / ID: 4qr8
TitleCrystal Structure of E coli pepQ
ComponentsXaa-Pro dipeptidase
KeywordsHYDROLASE / pepQ / Protease
Function / homology
Function and homology information


phosphoric triester hydrolase activity / Xaa-Pro dipeptidase / proline dipeptidase activity / metallodipeptidase activity / dipeptidase activity / peptide catabolic process / aminopeptidase activity / manganese ion binding / protein homodimerization activity / proteolysis / cytosol
Similarity search - Function
: / Xaa-Pro dipeptidase, N-terminal domain / Xaa-Pro dipeptidase / Peptidase M24B, X-Pro dipeptidase/aminopeptidase P, conserved site / Aminopeptidase P and proline dipeptidase signature. / Creatine Amidinohydrolase; Chain A, domain 1 / Creatinase/prolidase N-terminal domain / Creatinase/Aminopeptidase P/Spt16, N-terminal / Creatine Amidinohydrolase / Creatinase/methionine aminopeptidase superfamily ...: / Xaa-Pro dipeptidase, N-terminal domain / Xaa-Pro dipeptidase / Peptidase M24B, X-Pro dipeptidase/aminopeptidase P, conserved site / Aminopeptidase P and proline dipeptidase signature. / Creatine Amidinohydrolase; Chain A, domain 1 / Creatinase/prolidase N-terminal domain / Creatinase/Aminopeptidase P/Spt16, N-terminal / Creatine Amidinohydrolase / Creatinase/methionine aminopeptidase superfamily / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.999 Å
AuthorsPingwei, L.
CitationJournal: Plos One / Year: 2014
Title: Structural basis of substrate selectivity of E. coli prolidase.
Authors: Weaver, J. / Watts, T. / Li, P. / Rye, H.S.
History
DepositionJun 30, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Xaa-Pro dipeptidase
B: Xaa-Pro dipeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,5676
Polymers100,4702
Non-polymers974
Water23,6721314
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5100 Å2
ΔGint-65 kcal/mol
Surface area34570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.569, 97.440, 126.936
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Xaa-Pro dipeptidase / X-Pro dipeptidase / Imidodipeptidase / Proline dipeptidase / Prolidase


Mass: 50234.973 Da / Num. of mol.: 2 / Fragment: pepQ
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: pepQ, b3847, JW3823 / Production host: Escherichia coli (E. coli) / References: UniProt: P21165, Xaa-Pro dipeptidase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1314 / 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: 2.23 Å3/Da / Density % sol: 44.93 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M Bis-Tris, pH 6.5, 19% PEG MME 5000, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 61440 / Num. obs: 59597 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2→2.03 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.695 / Mean I/σ(I) obs: 2 / % possible all: 92.3

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.999→40.45 Å / SU ML: 0.22 / σ(F): 1.34 / σ(I): 0 / Phase error: 21.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2114 1995 3.35 %random
Rwork0.1729 ---
obs0.1742 59597 96.73 %-
all-61440 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.999→40.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7052 0 4 1314 8370
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047246
X-RAY DIFFRACTIONf_angle_d0.8029862
X-RAY DIFFRACTIONf_dihedral_angle_d11.3632634
X-RAY DIFFRACTIONf_chiral_restr0.0591066
X-RAY DIFFRACTIONf_plane_restr0.0031284
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9989-2.04890.31591330.27233819X-RAY DIFFRACTION91
2.0489-2.10430.27671370.24133934X-RAY DIFFRACTION94
2.1043-2.16620.24251420.21824078X-RAY DIFFRACTION96
2.1662-2.23610.23381380.22064014X-RAY DIFFRACTION96
2.2361-2.3160.27621370.24144009X-RAY DIFFRACTION95
2.316-2.40870.21371420.18514101X-RAY DIFFRACTION97
2.4087-2.51830.2691420.18144107X-RAY DIFFRACTION98
2.5183-2.65110.25051430.1844126X-RAY DIFFRACTION97
2.6511-2.81710.22181430.1814111X-RAY DIFFRACTION97
2.8171-3.03460.2121450.17594166X-RAY DIFFRACTION98
3.0346-3.33980.19791450.16224184X-RAY DIFFRACTION98
3.3398-3.82280.18071470.14214238X-RAY DIFFRACTION99
3.8228-4.81510.16781480.12924287X-RAY DIFFRACTION99
4.8151-40.45790.18111530.15844428X-RAY DIFFRACTION98
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)
10.29540.1192-0.22690.5759-0.4510.47840.0241-0.103-0.09790.0126-0.12790.0213-0.01230.2031-0.26070.0973-0.0094-0.02120.1723-0.00650.0548-19.32461.969511.0573
20.44850.0453-0.21670.30320.03180.26270.0038-0.06-0.1280.128-0.030.0214-0.00410.10630.00330.1357-0.0113-0.00280.13310.00310.105-22.7765-0.467412.4033
30.4133-0.04170.05160.3661-0.16910.0510.0306-0.0637-0.0882-0.1076-0.0111-0.0260.08650.03530.00510.11620.00690.00560.08470.00090.1066-6.40546.2269-15.6623
40.20260.4441-0.19570.8582-0.22740.2976-0.0198-0.00440.0361-0.0116-0.00060.0572-0.01260.0275-0.00060.0580.0021-0.01720.08180.00290.0815-8.759625.9559-12.6195
50.3492-0.067-0.13520.306-0.09650.3662-0.04470.21510.10370.0324-0.00390.0948-0.07320.0788-0.01140.0843-0.0205-0.0270.12970.0080.0907-38.7111.1559-20.9852
60.22660.02720.05410.18660.14390.3011-0.02990.05620.10310.01650.00180.1042-0.03590.056-0.00020.1113-0.0129-0.0160.10940.00280.1653-41.72923.2014-19.5027
70.6064-0.26650.09980.7793-0.2830.4573-0.05760.52330.00640.0307-0.1073-0.1936-0.15390.1836-0.18250.07130.00390.0364-0.0208-0.030.1014-15.8038-15.3254-17.3011
80.62360.07020.10410.5648-0.29090.20010.01640.0477-0.0731-0.02120.0043-0.040.0524-0.05340.00340.08230.01460.0010.0523-0.06310.0822-26.124-30.459-12.1737
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 83 )
2X-RAY DIFFRACTION2chain 'A' and (resid 84 through 163 )
3X-RAY DIFFRACTION3chain 'A' and (resid 164 through 268 )
4X-RAY DIFFRACTION4chain 'A' and (resid 269 through 443 )
5X-RAY DIFFRACTION5chain 'B' and (resid 3 through 88 )
6X-RAY DIFFRACTION6chain 'B' and (resid 89 through 163 )
7X-RAY DIFFRACTION7chain 'B' and (resid 164 through 235 )
8X-RAY DIFFRACTION8chain 'B' and (resid 236 through 443 )

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