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- PDB-3mru: Crystal Structure of Aminoacylhistidine Dipeptidase from Vibrio a... -

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Basic information

Entry
Database: PDB / ID: 3mru
TitleCrystal Structure of Aminoacylhistidine Dipeptidase from Vibrio alginolyticus
ComponentsAminoacyl-histidine dipeptidase
KeywordsHYDROLASE / METALLOPROTEASE / HOMODIMER
Function / homology
Function and homology information


Xaa-His dipeptidase / dipeptidase activity / metal ion binding
Similarity search - Function
Peptidase M20C, Xaa-His dipeptidase / Peptidase M20, dimerisation domain / Peptidase dimerisation domain / Peptidase M20 / Peptidase family M20/M25/M40 / Zn peptidases / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Aminoacyl-histidine dipeptidase
Similarity search - Component
Biological speciesVibrio alginolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsChang, C.-Y. / Hsieh, Y.-C. / Wu, T.-K. / Chen, C.-J.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Crystal structure and mutational analysis of aminoacylhistidine dipeptidase from vibrio alginolyticus reveal a new architecture of M20 metallopeptidases
Authors: Chang, C.-Y. / Hsieh, Y.-C. / Wang, T.-Y. / Chen, Y.-C. / Wang, Y.-K. / Chiang, T.-W. / Chen, Y.-J. / Chang, C.-H. / Chen, C.-J. / Wu, T.-K.
History
DepositionApr 29, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 1, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_seq_id / _struct_conn.ptnr2_label_asym_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

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Assembly

Deposited unit
A: Aminoacyl-histidine dipeptidase
B: Aminoacyl-histidine dipeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,5276
Polymers107,2652
Non-polymers2624
Water00
1
A: Aminoacyl-histidine dipeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7633
Polymers53,6331
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Aminoacyl-histidine dipeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7633
Polymers53,6331
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.407, 80.407, 303.095
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Aminoacyl-histidine dipeptidase / Xaa-His dipeptidase


Mass: 53632.668 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio alginolyticus (bacteria) / Plasmid: PET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q2LD50, Xaa-His dipeptidase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 53.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 28%(v/v) PEG 400, 0.2M Calcium chloride, 0.1M HEPES-Na buffer, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11101
21101
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL12B211
SYNCHROTRONNSRRC BL13B121
Detector
TypeIDDetectorDate
ADSC QUANTUM 4r1CCDAug 21, 2006
ADSC QUANTUM 3152CCDApr 29, 2006
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. obs: 21851 / % possible obs: 99.8 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.07 / Rsym value: 0.046 / Net I/σ(I): 17.6
Reflection shellResolution: 3→3.14 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.352 / Mean I/σ(I) obs: 4.8 / Num. unique all: 5431 / Rsym value: 0.32 / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
CNS1.21refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2QYV

2qyv


Resolution: 3→27.57 Å / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Details: Refmac was also used in refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.273 2174 9.8 %RANDOM
Rwork0.231 19669 --
obs-21843 98.9 %-
Solvent computationBsol: 75.712 Å2
Displacement parametersBiso max: 398.37 Å2 / Biso mean: 86.164 Å2 / Biso min: 22.98 Å2
Baniso -1Baniso -2Baniso -3
1-2.608 Å20 Å20 Å2
2--2.608 Å20 Å2
3----5.216 Å2
Refinement stepCycle: LAST / Resolution: 3→27.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7526 0 4 0 7530
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:ion.param

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