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- PDB-3wmr: Crystal structure of VinJ -

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Basic information

Entry
Database: PDB / ID: 3wmr
TitleCrystal structure of VinJ
ComponentsProline iminopeptidase
KeywordsHYDROLASE / alpha/beta hydrolase fold
Function / homology
Function and homology information


prolyl aminopeptidase / peptidase activity / proteolysis
Similarity search - Function
Proline-specific peptidase / Peptidase S33 / : / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE / prolyl aminopeptidase
Similarity search - Component
Biological speciesStreptomyces halstedii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsShinohara, Y. / Miyanaga, A. / Kudo, F. / Eguchi, T.
CitationJournal: Febs Lett. / Year: 2014
Title: The crystal structure of the amidohydrolase VinJ shows a unique hydrophobic tunnel for its interaction with polyketide substrates
Authors: Shinohara, Y. / Miyanaga, A. / Kudo, F. / Eguchi, T.
History
DepositionNov 22, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2014Group: Database references
Revision 1.2Nov 8, 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Proline iminopeptidase
B: Proline iminopeptidase
C: Proline iminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,7118
Polymers107,1103
Non-polymers6015
Water9,080504
1
A: Proline iminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9583
Polymers35,7031
Non-polymers2542
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Proline iminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0504
Polymers35,7031
Non-polymers3463
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Proline iminopeptidase


Theoretical massNumber of molelcules
Total (without water)35,7031
Polymers35,7031
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.870, 72.620, 75.450
Angle α, β, γ (deg.)114.02, 98.39, 98.50
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Proline iminopeptidase


Mass: 35703.352 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces halstedii (bacteria) / Gene: vinJ / Production host: Escherichia coli (E. coli) / References: UniProt: Q76KY6
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-P4G / 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE


Mass: 162.227 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 504 / 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: 2.38 Å3/Da / Density % sol: 48.29 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2M lithium acetate, 20% polyethylene glycol 3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 278K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 7, 2012
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→50.96 Å / Num. all: 71740 / Num. obs: 63636 / % possible obs: 88.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.95→2 Å / % possible all: 65.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.7.0029refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3NWO

3nwo


Resolution: 1.95→50.96 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.95 / SU B: 7.533 / SU ML: 0.106 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.172 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20576 3198 5 %RANDOM
Rwork0.16532 ---
all0.16737 68123 --
obs0.16737 60460 88.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.224 Å2
Baniso -1Baniso -2Baniso -3
1-4.91 Å20.37 Å2-0.22 Å2
2---1.94 Å2-0.08 Å2
3----1.82 Å2
Refinement stepCycle: LAST / Resolution: 1.95→50.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7047 0 40 504 7591
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0197298
X-RAY DIFFRACTIONr_bond_other_d0.0010.026750
X-RAY DIFFRACTIONr_angle_refined_deg1.2141.9539960
X-RAY DIFFRACTIONr_angle_other_deg0.774315540
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8085885
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.2323.478345
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.298151101
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4911548
X-RAY DIFFRACTIONr_chiral_restr0.0670.21080
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0218226
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021698
LS refinement shellResolution: 1.952→2.003 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 180 -
Rwork0.235 3298 -
obs--66.15 %
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)
10.1097-0.1506-0.06421.9198-0.53110.4087-0.01630.0009-0.0344-0.10180.02730.06610.0337-0.0235-0.0110.0209-0.0153-0.01210.0714-0.00640.1092-17.473736.0685-20.0853
20.1176-0.1038-0.03390.2732-0.06951.43270.0229-0.00170.01350.02370.05530.00770.0172-0.0223-0.07830.01760.00340.00470.0781-0.00570.091-10.565972.761-1.296
30.3115-0.19770.06061.02050.38160.5158-0.0282-0.0257-0.0169-0.10310.067-0.0346-0.03990.0672-0.03890.0224-0.01320.00610.0922-0.02030.0733-3.464940.304626.8518
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 299
2X-RAY DIFFRACTION1A401 - 402
3X-RAY DIFFRACTION2B4 - 299
4X-RAY DIFFRACTION2B400 - 402
5X-RAY DIFFRACTION3C4 - 299

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