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- PDB-3wwx: Crystal structure of D-stereospecific amidohydrolase from Strepto... -

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Basic information

Entry
Database: PDB / ID: 3wwx
TitleCrystal structure of D-stereospecific amidohydrolase from Streptomyces sp. 82F2
ComponentsS12 family peptidase
KeywordsHYDROLASE / Amidohydrolase
Function / homology
Function and homology information


: / Beta-lactamase-related / Beta-lactamase / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
OCTANE 1,8-DIAMINE / S12 family peptidase
Similarity search - Component
Biological speciesStreptomyces sp. 82F2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.49 Å
AuthorsArima, J. / Nagano, S. / Hino, T. / Shimone, K. / Isoda, Y. / Mori, N.
CitationJournal: Febs J. / Year: 2016
Title: Crystal structure of D-stereospecific amidohydrolase from Streptomyces sp. 82F2 - insight into the structural factors for substrate specificity.
Authors: Arima, J. / Shimone, K. / Miyatani, K. / Tsunehara, Y. / Isoda, Y. / Hino, T. / Nagano, S.
History
DepositionJul 3, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 8, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Aug 24, 2022Group: Database references / Derived calculations / Category: citation / database_2 / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: S12 family peptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5852
Polymers37,4411
Non-polymers1441
Water7,800433
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.290, 74.681, 76.447
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 S12 family peptidase


Mass: 37440.941 Da / Num. of mol.: 1 / Fragment: UNP residues 34-382
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. 82F2 (bacteria) / Gene: s12ap / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: E2RVJ1
#2: Chemical ChemComp-DIA / OCTANE 1,8-DIAMINE / 1,8-DIAMINOOCTANE / OCTAMETHYLENEDIAMINE / 1,8-OCTANEDIAMINE


Mass: 144.258 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H20N2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 433 / 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: 2.26 Å3/Da / Density % sol: 45.58 % / Mosaicity: 0.404 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 1.5 M Citrate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: Saturn A200 / Detector: CCD / Date: Dec 17, 2011
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.49→50 Å / Num. all: 56122 / Num. obs: 54112 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Biso Wilson estimate: 14.91 Å2 / Rmerge(I) obs: 0.053 / Χ2: 2.189 / Net I/σ(I): 20
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.49-1.522.70.24420060.9273.5
1.52-1.5430.2222061.01780.1
1.54-1.573.30.19923831.18785.9
1.57-1.613.60.17425611.21491.9
1.61-1.644.10.17127091.26397.8
1.64-1.684.80.15427421.36299.6
1.68-1.7260.14527761.585100
1.72-1.776.90.14127671.84399.9
1.77-1.8270.12228061.93100
1.82-1.8870.10827892.119100
1.88-1.9470.09627712.195100
1.94-2.0270.08428072.437100
2.02-2.116.90.07527912.6100
2.11-2.236.90.06828012.755100
2.23-2.376.90.06528222.795100
2.37-2.556.90.05928182.782100
2.55-2.86.90.05628252.815100
2.8-3.216.80.04828502.653100
3.21-4.046.70.0428832.526100
4.04-506.10.03229991.73698.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: EP_AUTO

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.5.5phasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.14data extraction
BSSdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CEF

1cef


Resolution: 1.49→29.511 Å / FOM work R set: 0.911 / SU ML: 0.11 / σ(F): 1.36 / Phase error: 15.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1616 2728 5.05 %RANDOM
Rwork0.1408 ---
all0.149 56149 --
obs0.1419 54049 96.26 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 79.48 Å2 / Biso mean: 17.4 Å2 / Biso min: 7.1 Å2
Refinement stepCycle: LAST / Resolution: 1.49→29.511 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2549 0 10 433 2992
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092616
X-RAY DIFFRACTIONf_angle_d1.3153550
X-RAY DIFFRACTIONf_chiral_restr0.074390
X-RAY DIFFRACTIONf_plane_restr0.007468
X-RAY DIFFRACTIONf_dihedral_angle_d14.025945
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4895-1.51660.23661010.17561937203871
1.5166-1.54570.19561130.16132223233680
1.5457-1.57730.16371240.14852411253587
1.5773-1.61160.16151350.14362576271193
1.6116-1.64910.17991590.14182720287998
1.6491-1.69030.16631360.141827712907100
1.6903-1.7360.16871380.138327952933100
1.736-1.78710.16511250.136627982923100
1.7871-1.84480.15171280.133327972925100
1.8448-1.91070.17221780.13328022980100
1.9107-1.98720.17011560.13627612917100
1.9872-2.07760.14721680.132227712939100
2.0776-2.18710.15951450.125628092954100
2.1871-2.32410.13851290.126128232952100
2.3241-2.50340.13931500.129628222972100
2.5034-2.75520.15041660.133428042970100
2.7552-3.15350.16311510.142128583009100
3.1535-3.97150.15791520.138828813033100
3.9715-29.51710.17721740.16642962313699

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