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- PDB-2p91: Crystal structure of Enoyl-[acyl-carrier-protein] reductase (NADH... -

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Basic information

Entry
Database: PDB / ID: 2p91
TitleCrystal structure of Enoyl-[acyl-carrier-protein] reductase (NADH) from Aquifex aeolicus VF5
ComponentsEnoyl-[acyl-carrier-protein] reductase [NADH]
KeywordsOXIDOREDUCTASE / NADH-dependent enoyl-ACP reductase / aq_1552 / fabI / Aquifex aeolicus VF5 / Structural Genomics / PSI / Protein Structure Initiative / Southeast Collaboratory for Structural Genomics / SECSG / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE / RSGI
Function / homology
Function and homology information


enoyl-[acyl-carrier-protein] reductase activity (NAD(P)H) / fatty acid elongation / enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / identical protein binding
Similarity search - Function
Enoyl-[acyl-carrier-protein] reductase (NADH) / 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
Enoyl-[acyl-carrier-protein] reductase [NADH] FabI
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsChen, L. / Li, Y. / Ebihara, A. / Shinkai, A. / Kuramitsu, S. / Yokoyama, S. / Zhao, M. / Rose, J.P. / Wang, B.-C. / Southeast Collaboratory for Structural Genomics (SECSG) / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of Enoyl-[acyl-carrier-protein] reductase (NADH) from Aquifex aeolicus VF5
Authors: Chen, L. / Li, Y. / Ebihara, A. / Shinkai, A. / Kuramitsu, S. / Yokoyama, S. / Zhao, M. / Rose, J.P. / Wang, B.-C.
History
DepositionMar 23, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.5Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999 SEQUENCE AUTHORS STATE THAT THE PRESENCE OF N-TERMINAL 15 AMINO ACIDS RESIDUES IS DERIVED FROM THE ... SEQUENCE AUTHORS STATE THAT THE PRESENCE OF N-TERMINAL 15 AMINO ACIDS RESIDUES IS DERIVED FROM THE DIFFERENCE IN GENOME ANNOTATION BETWEEN UNIPROT AND GENBANK SEQUENCES.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Enoyl-[acyl-carrier-protein] reductase [NADH]
B: Enoyl-[acyl-carrier-protein] reductase [NADH]
C: Enoyl-[acyl-carrier-protein] reductase [NADH]
D: Enoyl-[acyl-carrier-protein] reductase [NADH]


Theoretical massNumber of molelcules
Total (without water)126,1454
Polymers126,1454
Non-polymers00
Water11,602644
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14020 Å2
ΔGint-91 kcal/mol
Surface area32670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.078, 119.019, 119.197
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a tetramer in the asymmetric unit.

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Components

#1: Protein
Enoyl-[acyl-carrier-protein] reductase [NADH] / NADH-dependent enoyl-ACP reductase


Mass: 31536.371 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Gene: fabI, aq_1552 / Plasmid: pET-21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL
References: UniProt: O67505, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 644 / 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: 2.03 Å3/Da / Density % sol: 39.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: USING 2 MICROLITER DROPS CONTAINING EQUAL VOLUMES OF PROTEIN CONCENTRATE (10.93 mg/ml) AND RESERVOIR SOLUTION CONTAINING 0.1 M Phosphate-citrate (pH 4.2), 40% v/v PEG200, 0.15 M Sodium ...Details: USING 2 MICROLITER DROPS CONTAINING EQUAL VOLUMES OF PROTEIN CONCENTRATE (10.93 mg/ml) AND RESERVOIR SOLUTION CONTAINING 0.1 M Phosphate-citrate (pH 4.2), 40% v/v PEG200, 0.15 M Sodium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.97243 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 24, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97243 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 70158 / % possible obs: 99.9 % / Redundancy: 11.1 % / Rsym value: 0.089 / Χ2: 1.44 / Net I/σ(I): 10
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2-2.0710.80.24268860.641100
2.07-2.15110.19869560.681100
2.15-2.25110.16669500.7661100
2.25-2.3711.10.14269240.8261100
2.37-2.5211.20.12269810.9571100
2.52-2.7111.20.10669891.0861100
2.71-2.9911.30.09269881.3631100
2.99-3.4211.50.0870471.961100
3.42-4.3111.20.07271052.9821100
4.31-5010.80.0673322.991199.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
SERGUIdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1JW7

1jw7
PDB Unreleased entry


Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.935 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.167 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.197 3528 5 %RANDOM
Rwork0.167 ---
obs0.169 70088 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.638 Å2
Baniso -1Baniso -2Baniso -3
1--0.98 Å20 Å20 Å2
2--0.61 Å20 Å2
3---0.37 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7456 0 0 644 8100
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0227596
X-RAY DIFFRACTIONr_angle_refined_deg1.1611.9610262
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9465959
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.06423.484310
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.788151322
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3071544
X-RAY DIFFRACTIONr_chiral_restr0.0830.21176
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025594
X-RAY DIFFRACTIONr_nbd_refined0.20.23702
X-RAY DIFFRACTIONr_nbtor_refined0.3030.25316
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2632
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1950.2249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.150.268
X-RAY DIFFRACTIONr_mcbond_it0.691.54765
X-RAY DIFFRACTIONr_mcangle_it1.16827640
X-RAY DIFFRACTIONr_scbond_it1.80632831
X-RAY DIFFRACTIONr_scangle_it2.9614.52622
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.215 264 -
Rwork0.165 4770 -
obs-5034 98.24 %

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