[English] 日本語
Yorodumi
- PDB-4i08: Crystal structure of beta-ketoacyl-acyl carrier protein reductase... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4i08
TitleCrystal structure of beta-ketoacyl-acyl carrier protein reductase (FabG) from Vibrio cholerae in complex with NADPH
Components3-oxoacyl-[acyl-carrier-protein] reductase FabG
KeywordsOXIDOREDUCTASE / STRUCTURAL GENOMICS / CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES / CSGID / Vibrio cholerae / FabG / Rossmann fold / beta-ketoacyl-acyl carrier protein reductase / short chain dehydrogenase / NADP(H)
Function / homology
Function and homology information


3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / fatty acid elongation / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / NAD binding / NADP binding
Similarity search - Function
3-oxoacyl-(acyl-carrier-protein) reductase / : / PKS_KR / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold ...3-oxoacyl-(acyl-carrier-protein) reductase / : / PKS_KR / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-NDP / 3-oxoacyl-[acyl-carrier-protein] reductase FabG
Similarity search - Component
Biological speciesVibrio cholerae O1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.063 Å
AuthorsHou, J. / Chruszcz, M. / Zheng, H. / Osinski, T. / Anderson, W.F. / Minor, W. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: J.Bacteriol. / Year: 2015
Title: Dissecting the Structural Elements for the Activation of beta-Ketoacyl-(Acyl Carrier Protein) Reductase from Vibrio cholerae.
Authors: Hou, J. / Zheng, H. / Chruszcz, M. / Zimmerman, M.D. / Shumilin, I.A. / Osinski, T. / Demas, M. / Grimshaw, S. / Minor, W.
History
DepositionNov 16, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2015Group: Database references
Revision 1.2Jan 27, 2016Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Revision 1.4Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _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
Revision 1.5Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 3-oxoacyl-[acyl-carrier-protein] reductase FabG
B: 3-oxoacyl-[acyl-carrier-protein] reductase FabG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,29216
Polymers52,7162
Non-polymers2,57614
Water2,306128
1
A: 3-oxoacyl-[acyl-carrier-protein] reductase FabG
B: 3-oxoacyl-[acyl-carrier-protein] reductase FabG
hetero molecules

A: 3-oxoacyl-[acyl-carrier-protein] reductase FabG
B: 3-oxoacyl-[acyl-carrier-protein] reductase FabG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,58432
Polymers105,4324
Non-polymers5,15128
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_445-x-1,-y-1,z1
Buried area22630 Å2
ΔGint-280 kcal/mol
Surface area32370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.941, 63.941, 190.374
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number171
Space group name H-MP62
Components on special symmetry positions
IDModelComponents
11A-445-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: _ / Auth seq-ID: 2 - 248 / Label seq-ID: 5 - 251

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

-
Components

#1: Protein 3-oxoacyl-[acyl-carrier-protein] reductase FabG / 3-ketoacyl-acyl carrier protein reductase / Beta-Ketoacyl-acyl carrier protein reductase / Beta- ...3-ketoacyl-acyl carrier protein reductase / Beta-Ketoacyl-acyl carrier protein reductase / Beta-ketoacyl-ACP reductase


Mass: 26358.113 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O1 (bacteria) / Strain: ATCC 39315 / El Tor Inaba N16961 / Gene: fabG, VC2021, VC_2021 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL
References: UniProt: Q9KQH7, 3-oxoacyl-[acyl-carrier-protein] reductase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.13 Å3/Da / Density % sol: 42.28 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 9
Details: 2.7M Ammonium Sulfate, 0.1M Tris-HCl, 2% PEG400, pH 9, VAPOR DIFFUSION, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 18, 2011 / Details: MIRRORS
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionRedundancy: 5.6 % / Av σ(I) over netI: 26.95 / Number: 151910 / Rmerge(I) obs: 0.102 / Χ2: 3.18 / D res high: 2.06 Å / D res low: 50 Å / Num. obs: 27006 / % possible obs: 99.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.595099.910.0495.1846.1
4.445.5999.910.0552.8176
3.884.4499.910.0765.1085.7
3.523.8899.810.0622.8565.7
3.273.5299.910.0853.4635.6
3.083.2710010.0871.9665.7
2.923.0899.910.112.2885.6
2.82.9210010.1311.6065.6
2.692.810010.1511.4495.7
2.62.6999.910.2983.9085.6
2.512.699.910.2412.3065.7
2.442.5199.810.1991.3245.7
2.382.4410010.2761.5955.7
2.322.3899.910.3432.8895.6
2.272.3299.810.4072.6795.6
2.222.2710010.4983.6185.7
2.172.2210010.5163.4995.6
2.132.1710010.5484.9535.5
2.12.1399.910.4831.1245
2.062.110010.8119.724.9
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.52
11K, H, -L20.48
ReflectionResolution: 2.06→50 Å / Num. obs: 27006 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Biso Wilson estimate: 20.5 Å2 / Rmerge(I) obs: 0.102 / Χ2: 3.18 / Net I/σ(I): 9.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.06-2.14.90.81113249.721100
2.1-2.1350.48313841.124199.9
2.13-2.175.50.54813264.9531100
2.17-2.225.60.51613373.4991100
2.22-2.275.70.49813613.6181100
2.27-2.325.60.40713202.679199.8
2.32-2.385.60.34313662.889199.9
2.38-2.445.70.27613631.5951100
2.44-2.515.70.19913231.324199.8
2.51-2.65.70.24113552.306199.9
2.6-2.695.60.29813343.908199.9
2.69-2.85.70.15113491.4491100
2.8-2.925.60.13113681.6061100
2.92-3.085.60.1113362.288199.9
3.08-3.275.70.08713411.9661100
3.27-3.525.60.08513723.463199.9
3.52-3.885.70.06213292.856199.8
3.88-4.445.70.07613645.108199.9
4.44-5.5960.05513582.817199.9
5.59-506.10.04913965.184199.9

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3RRO

3rro


Resolution: 2.063→47.86 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.961 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 4.589 / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.041 / ESU R Free: 0.029 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.171 1330 4.9 %RANDOM
Rwork0.1526 ---
obs0.1535 26944 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 101.98 Å2 / Biso mean: 38.6873 Å2 / Biso min: 16.98 Å2
Baniso -1Baniso -2Baniso -3
1-11.87 Å20 Å20 Å2
2--11.87 Å20 Å2
3----23.75 Å2
Refinement stepCycle: LAST / Resolution: 2.063→47.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3546 0 154 128 3828
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0193735
X-RAY DIFFRACTIONr_bond_other_d0.0030.023587
X-RAY DIFFRACTIONr_angle_refined_deg1.3432.0115063
X-RAY DIFFRACTIONr_angle_other_deg0.82538213
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8045486
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.33124.599137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.03615619
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.7491525
X-RAY DIFFRACTIONr_chiral_restr0.0720.2603
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024208
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02791
Refine LS restraints NCS

Ens-ID: 1 / Number: 14329 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.04 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.063→2.117 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 95 -
Rwork0.208 1851 -
all-1946 -
obs--98.13 %
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)
12.48720.62510.03591.07491.19913.7432-0.0232-0.03250.1218-0.04850.2037-0.2123-0.03170.1087-0.18040.0811-0.04310.00750.1180.00010.17686.85-13.3812.357
21.6960.9292-0.1441.4179-0.35141.1376-0.21880.30450.1212-0.13080.1649-0.0675-0.23470.15620.05390.1215-0.06980.0170.14510.00840.1302-2.673-16.074-9.556
31.39530.59810.11370.4313-0.2370.5171-0.04870.1465-0.07-0.04830.0621-0.0343-0.010.0428-0.01340.0774-0.0186-0.00110.104-0.0080.1542-6.532-26.452-0.79
41.46730.7165-0.63431.29690.46361.01720.08570.14970.2154-0.00710.00790.0677-0.1595-0.0505-0.09360.0952-0.00760.00350.09030.04270.14-7.855-14.3689.816
52.92980.9807-0.96132.0072-0.18722.2571-0.0106-0.03010.11520.0990.063-0.2696-0.11190.1148-0.05240.1033-0.0531-0.03690.0646-0.0030.18117.811-14.99727.79
61.95080.64560.79970.97220.20371.15710.1347-0.2443-0.0520.2313-0.1654-0.1131-0.04520.08710.03080.169-0.0528-0.03690.0888-0.00310.11370.754-21.77439.808
70.99030.5775-0.05150.4168-0.17880.58020.0943-0.0649-0.01460.1618-0.0681-0.0235-0.09640.002-0.02620.1949-0.0477-0.02880.03840.00650.1556-7.563-23.42829.159
80.81730.03920.15811.30160.57950.32430.05350.0981-0.06260.0936-0.0366-0.08990.00330.0439-0.01680.1009-0.0322-0.02640.06910.00840.1528-0.507-24.90917.864
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 39
2X-RAY DIFFRACTION2A40 - 106
3X-RAY DIFFRACTION3A107 - 175
4X-RAY DIFFRACTION4A176 - 248
5X-RAY DIFFRACTION5B2 - 39
6X-RAY DIFFRACTION6B40 - 106
7X-RAY DIFFRACTION7B107 - 205
8X-RAY DIFFRACTION8B206 - 248

+
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