[English] 日本語
Yorodumi
- PDB-5bov: Crystal structure of a putative epoxide hydrolase (KPN_01808) fro... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5bov
TitleCrystal structure of a putative epoxide hydrolase (KPN_01808) from Klebsiella pneumoniae subsp. pneumoniae MGH 78578 at 1.60 A resolution
ComponentsPutative epoxide hydrolase protein
KeywordsHYDROLASE / putative epoxide hydrolase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Function and homology information


acylglycerol catabolic process / monoacylglycerol lipase activity / membrane
Similarity search - Function
: / Epoxide hydrolase-like / 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
Epoxide hydrolase protein
Similarity search - Component
Biological speciesKlebsiella pneumoniae subsp. pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a putative epoxide hydrolase (KPN_01808) from Klebsiella pneumoniae subsp. pneumoniae MGH 78578 at 1.60 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMay 27, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Advisory / Derived calculations ...Advisory / Derived calculations / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_struct_oper_list ...entity_src_gen / pdbx_struct_oper_list / pdbx_validate_symm_contact / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Feb 1, 2023Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative epoxide hydrolase protein
B: Putative epoxide hydrolase protein
C: Putative epoxide hydrolase protein
D: Putative epoxide hydrolase protein


Theoretical massNumber of molelcules
Total (without water)134,4014
Polymers134,4014
Non-polymers00
Water33,8681880
1
A: Putative epoxide hydrolase protein


Theoretical massNumber of molelcules
Total (without water)33,6001
Polymers33,6001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative epoxide hydrolase protein


Theoretical massNumber of molelcules
Total (without water)33,6001
Polymers33,6001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Putative epoxide hydrolase protein


Theoretical massNumber of molelcules
Total (without water)33,6001
Polymers33,6001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Putative epoxide hydrolase protein


Theoretical massNumber of molelcules
Total (without water)33,6001
Polymers33,6001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Putative epoxide hydrolase protein

C: Putative epoxide hydrolase protein


Theoretical massNumber of molelcules
Total (without water)67,2012
Polymers67,2012
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area2340 Å2
ΔGint-19 kcal/mol
Surface area22590 Å2
MethodPISA
6
B: Putative epoxide hydrolase protein

D: Putative epoxide hydrolase protein


Theoretical massNumber of molelcules
Total (without water)67,2012
Polymers67,2012
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_454x-1,y,z-11
Buried area2330 Å2
ΔGint-19 kcal/mol
Surface area22770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.199, 81.866, 89.925
Angle α, β, γ (deg.)101.000, 106.900, 100.840
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
Putative epoxide hydrolase protein


Mass: 33600.285 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578) (bacteria)
Strain: ATCC 700721 / MGH 78578 / Gene: KPN_01808 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: A6T9G8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1880 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT (36-338) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THE CONSTRUCT (36-338) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 43.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M bicine pH 9, 30% polyethylene glycol 6000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.97907 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 26, 2015
Details: Vertical focusing mirror; double crystal Si(111) monochromator
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97907 Å / Relative weight: 1
ReflectionResolution: 1.6→42.848 Å / Num. obs: 146333 / % possible obs: 96.8 % / Observed criterion σ(I): -3 / Redundancy: 3.916 % / Biso Wilson estimate: 15.778 Å2 / Rmerge F obs: 0.998 / Rmerge(I) obs: 0.078 / Rrim(I) all: 0.091 / Net I/σ(I): 11.66 / Num. measured all: 572981
Reflection shell
Resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) allDiffraction-ID% possible all
1.6-1.660.7560.65525921615811150550.758195.2
1.66-1.720.8250.5262.55123313640130290.60995.5
1.72-1.80.8970.3863.45851315499148640.44795.9
1.8-1.90.9440.2694.86022915930153090.31296.1
1.9-2.020.9760.1737.35727015117146080.20196.6
2.02-2.170.9880.11710.55509414531140820.13696.9
2.17-2.390.9930.08913.45756215194147870.10497.3
2.39-2.730.9960.06916.95704014974146270.0897.7
2.73-3.440.9980.044245827815186149270.05198.3
3.44-42.8480.9990.03230.65854615228150450.03798.8

-
Phasing

PhasingMethod: SAD

-
Processing

Software
NameVersionClassification
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XDSdata reduction
XSCALENovember 3, 2014 BUILT=20141118data scaling
REFMAC5.8.0107refinement
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→42.848 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.966 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 3.449 / SU ML: 0.059 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.085 / ESU R Free: 0.082
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED ...Details: 1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 2. THE MAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT. 3. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 4. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS.
RfactorNum. reflection% reflectionSelection details
Rfree0.1739 7372 5 %RANDOM
Rwork0.1485 138956 --
obs0.1498 146328 96.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 73.46 Å2 / Biso mean: 17.638 Å2 / Biso min: 5.35 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å2-0.49 Å2-0.51 Å2
2--0.22 Å20.04 Å2
3---0.09 Å2
Refinement stepCycle: LAST / Resolution: 1.6→42.848 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9395 0 0 1880 11275
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0199843
X-RAY DIFFRACTIONr_bond_other_d0.0130.029140
X-RAY DIFFRACTIONr_angle_refined_deg1.7851.93913485
X-RAY DIFFRACTIONr_angle_other_deg1.91320967
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.05651241
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.86823.354480
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.562151415
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1281575
X-RAY DIFFRACTIONr_chiral_restr0.1090.21408
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.02111495
X-RAY DIFFRACTIONr_gen_planes_other0.0110.022454
X-RAY DIFFRACTIONr_mcbond_it0.8821.0434838
X-RAY DIFFRACTIONr_mcbond_other0.8811.0434837
X-RAY DIFFRACTIONr_mcangle_it1.3971.5616052
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 529 -
Rwork0.253 10164 -
all-10693 -
obs--95.04 %
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)
10.40180.20960.24250.3028-0.03270.5315-0.00450.047-0.04430.0110.035-0.0197-0.02670.046-0.03050.01030.00570.00040.0223-0.01090.008713.9308-7.537140.4715
20.29830.09820.0750.3135-0.08710.4148-0.0371-0.00040.01380.00520.0344-0.0134-0.0107-0.00160.00280.01470.0042-0.00910.0078-0.00250.006934.9272-35.6327-0.7875
30.2391-0.03690.23530.4925-0.40510.72090.0314-0.00910.0145-0.00040.00810.05250.0377-0.0043-0.03950.0094-0.00080.00290.0093-0.00150.008140.23545.45671.8599
40.45930.44770.37711.2296-0.30091.0845-0.0135-0.05840.0952-0.0880.02880.16280.0976-0.1211-0.01530.0167-0.0082-0.01610.0263-0.00390.031134.9545-47.099643.2845
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A38 - 338
2X-RAY DIFFRACTION2B37 - 338
3X-RAY DIFFRACTION3C41 - 338
4X-RAY DIFFRACTION4D41 - 338

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more