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- PDB-3i7m: N-terminal domain of Xaa-Pro dipeptidase from Lactobacillus brevis. -

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Basic information

Entry
Database: PDB / ID: 3i7m
TitleN-terminal domain of Xaa-Pro dipeptidase from Lactobacillus brevis.
ComponentsXaa-Pro dipeptidase
KeywordsHYDROLASE / structural genomics / APC64794.2 / Xaa-Pro dipeptidase / Metallo peptidase / Creatinase/Prolidase N-terminal domain / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


metalloexopeptidase activity / aminopeptidase activity
Similarity search - Function
: / Creatinase, N-terminal / Creatinase/Prolidase N-terminal domain / Creatine Amidinohydrolase; Chain A, domain 1 / Creatinase/prolidase N-terminal domain / Creatinase/Aminopeptidase P/Spt16, N-terminal / Peptidase M24, methionine aminopeptidase / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like ...: / Creatinase, N-terminal / Creatinase/Prolidase N-terminal domain / Creatine Amidinohydrolase; Chain A, domain 1 / Creatinase/prolidase N-terminal domain / Creatinase/Aminopeptidase P/Spt16, N-terminal / Peptidase M24, methionine aminopeptidase / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Mername-AA019 peptidase. Metallo peptidase. MEROPS family M24B
Similarity search - Component
Biological speciesLactobacillus brevis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.46 Å
AuthorsOsipiuk, J. / Xu, X. / Cui, H. / Ng, J. / Savchenko, A. / Edwards, A.M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: X-ray crystal structure of N-terminal domain of Xaa-Pro dipeptidase from Lactobacillus brevis.
Authors: Osipiuk, J. / Xu, X. / Cui, H. / Ng, J. / Savchenko, A. / Edwards, A.M. / Joachimiak, A.
History
DepositionJul 8, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Xaa-Pro dipeptidase


Theoretical massNumber of molelcules
Total (without water)16,1221
Polymers16,1221
Non-polymers00
Water3,477193
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.867, 50.962, 49.289
Angle α, β, γ (deg.)90.000, 104.330, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Xaa-Pro dipeptidase / Mername-AA019 peptidase. Metallo peptidase. MEROPS family M24B


Mass: 16122.450 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus brevis (bacteria) / Strain: ATCC 367 / Gene: LVIS_1204 / Plasmid: pET15b modified / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q03R62
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.03 Å3/Da / Density % sol: 39.49 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris buffer, 0.2 M ammonium sulfate, 25% PEG-3350, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 29, 2009
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.46→36.5 Å / Num. all: 22642 / Num. obs: 22642 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.1 % / Biso Wilson estimate: 27 Å2 / Rmerge(I) obs: 0.053 / Χ2: 1.561 / Net I/σ(I): 14.6
Reflection shellResolution: 1.46→1.49 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.05 / Num. unique all: 1115 / Χ2: 0.987 / % possible all: 98.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0054refinement
PDB_EXTRACT3.005data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
SHELXDphasing
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.46→36.5 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.956 / Occupancy max: 1 / Occupancy min: 0.24 / SU B: 2.605 / SU ML: 0.045 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.071 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.198 1149 5.1 %RANDOM
Rwork0.163 ---
all0.164 22596 --
obs0.164 22596 99.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 50.09 Å2 / Biso mean: 16.355 Å2 / Biso min: 5.11 Å2
Baniso -1Baniso -2Baniso -3
1-0.37 Å20 Å20.38 Å2
2---0.33 Å20 Å2
3---0.15 Å2
Refinement stepCycle: LAST / Resolution: 1.46→36.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1077 0 0 193 1270
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0221229
X-RAY DIFFRACTIONr_bond_other_d0.0010.02803
X-RAY DIFFRACTIONr_angle_refined_deg1.7911.9271699
X-RAY DIFFRACTIONr_angle_other_deg0.99831993
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0725163
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.9625.67267
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.66415205
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.763153
X-RAY DIFFRACTIONr_chiral_restr0.1090.2183
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211415
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02241
X-RAY DIFFRACTIONr_mcbond_it1.1071.5731
X-RAY DIFFRACTIONr_mcbond_other0.3641.5284
X-RAY DIFFRACTIONr_mcangle_it1.80321206
X-RAY DIFFRACTIONr_scbond_it2.713498
X-RAY DIFFRACTIONr_scangle_it4.1234.5479
LS refinement shellResolution: 1.456→1.494 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 79 -
Rwork0.275 1515 -
all-1594 -
obs-1594 95.05 %
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)
11.8307-1.0189-0.19761.9316-0.09560.70590.16620.06490.0519-0.1267-0.12990.0571-0.0894-0.0474-0.03630.06670.0524-0.00550.0487-0.00630.03249.8135.35610.3614
21.7196-0.56550.28691.43550.46071.17460.13990.0395-0.1126-0.1098-0.10720.0102-0.0402-0.0179-0.03270.04670.0199-0.01030.0333-0.0060.061915.8872-3.427614.8207
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 90
2X-RAY DIFFRACTION2A91 - 135

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