[English] 日本語
Yorodumi
- PDB-3k31: Crystal structure of eonyl-(acyl-carrier-protein) reductase from ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3k31
TitleCrystal structure of eonyl-(acyl-carrier-protein) reductase from anaplasma phagocytophilum in complex with nad at 1.9a resolution
ComponentsEnoyl-(Acyl-carrier-protein) reductase
KeywordsOXIDOREDUCTASE / SSGCID / NIH / NIAID / SBRI / UW / DECODE / EONYL-(ACYL-CARRIER-PROTEIN) REDUCTASE / ANAPLASMA PHAGOCYTOPHILUM / NAD / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / fatty acid biosynthetic process / nucleotide binding
Similarity search - Function
Enoyl-[acyl-carrier-protein] reductase (NADH) / 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Enoyl-[acyl-carrier-protein] reductase [NADH]
Similarity search - Component
Biological speciesAnaplasma phagocytophilum (agent of human granulocytic ehrlichiosis)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of eonyl-(acyl-carrier-protein) reductase from anaplasma phagocytophilum in complex with nad at 1.9a resolution
Authors: SSGCID / Abendroth, J. / Arakaki, T. / Staker, B.
History
DepositionSep 30, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Sep 6, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Enoyl-(Acyl-carrier-protein) reductase
B: Enoyl-(Acyl-carrier-protein) reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,8538
Polymers63,8192
Non-polymers1,0346
Water6,557364
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-21 kcal/mol
Surface area21730 Å2
MethodPISA
2
A: Enoyl-(Acyl-carrier-protein) reductase
B: Enoyl-(Acyl-carrier-protein) reductase
hetero molecules

A: Enoyl-(Acyl-carrier-protein) reductase
B: Enoyl-(Acyl-carrier-protein) reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,70516
Polymers127,6384
Non-polymers2,06812
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area18080 Å2
ΔGint-92 kcal/mol
Surface area34730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.780, 89.730, 79.110
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-418-

HOH

Detailsauthors state that the BIOLOGICAL UNIT IS A DIMER

-
Components

#1: Protein Enoyl-(Acyl-carrier-protein) reductase


Mass: 31909.375 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anaplasma phagocytophilum (agent of human granulocytic ehrlichiosis)
Strain: HZ / Gene: fabI, APH_0473 / Plasmid: AVA0421 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q2GKM8, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 364 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsNAD WAS USED FOR CO-CRYSTALLIZATION, HOWEVER ONLY THE AMP MOIETY COULD BE OBSERVED.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.24 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8
Details: JCSG+ SCREEN CONDITION E11: 100MM IMIDAZOLE PH 80, 10% PEG 8000; ANPHA.00817.A AT 23MG/ML WITH 1MM NAD, PH 8.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97351 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Sep 18, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97351 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 53969 / Num. obs: 53869 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 27.36 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 20.74
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 3924 % / Rmerge(I) obs: 0.491 / Mean I/σ(I) obs: 5.6 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
REFMAC5.5.0104refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: native structure, pdb entry 3k2e

3k2e


Resolution: 1.8→19.78 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.959 / SU B: 3.993 / SU ML: 0.057 / Isotropic thermal model: isotropic, TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.096 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.175 2709 5 %RANDOM
Rwork0.148 ---
all0.15 53869 --
obs0.15 53867 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.54 Å2
Baniso -1Baniso -2Baniso -3
1-0.37 Å20 Å20 Å2
2--0.24 Å20 Å2
3----0.61 Å2
Refinement stepCycle: LAST / Resolution: 1.8→19.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3825 0 47 364 4236
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0224008
X-RAY DIFFRACTIONr_bond_other_d0.0010.022524
X-RAY DIFFRACTIONr_angle_refined_deg1.5231.9675469
X-RAY DIFFRACTIONr_angle_other_deg1.00336222
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4745543
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.35624.507142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.91115616
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9641511
X-RAY DIFFRACTIONr_chiral_restr0.0920.2645
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024518
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02784
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9691.52609
X-RAY DIFFRACTIONr_mcbond_other0.2731.51088
X-RAY DIFFRACTIONr_mcangle_it1.77124167
X-RAY DIFFRACTIONr_scbond_it2.77631399
X-RAY DIFFRACTIONr_scangle_it4.5934.51290
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.222 204 -
Rwork0.182 3688 -
obs--99.95 %
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)
10.2553-0.04870.00220.20020.09090.32620.02610.03310.0471-0.0655-0.0237-0.0061-0.0562-0.0163-0.00230.03530.0038-0.00610.01090.0140.022436.728414.773464.3466
20.1122-0.11290.02410.2481-0.03390.2876-0.0267-0.04020.00340.04010.02690.037-0.0373-0.0439-0.00030.01170.01080.0040.0366-0.01670.019929.20179.405395.1452
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999

+
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