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- PDB-3k2e: Crystal structure of enoyl-(acyl-carrier-protein) reductase from ... -

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Basic information

Entry
Database: PDB / ID: 3k2e
TitleCrystal structure of enoyl-(acyl-carrier-protein) reductase from Anaplasma phagocytophilum at 1.9A resolution
ComponentsEnoyl-(Acyl-carrier-protein) reductase
KeywordsOXIDOREDUCTASE / SSGCID / NIH / NIAID / SBRI / UW / DECODE / EONYL-(ACYL-CARRIER-PROTEIN) REDUCTASE / ANAPLASMA PHAGOCYTOPHILUM / 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
Enoyl-[acyl-carrier-protein] reductase [NADH]
Similarity search - Component
Biological speciesAnaplasma phagocytophilum (agent of human granulocytic ehrlichiosis)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsAbendroth, J. / Staker, B. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of enoyl-(acyl-carrier-protein) reductase from Anaplasma phagocytophilum at 1.9A resolution
Authors: Abendroth, J. / Staker, B.
History
DepositionSep 30, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / 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

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


Theoretical massNumber of molelcules
Total (without water)64,49711
Polymers63,8192
Non-polymers6799
Water5,819323
1
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)128,99522
Polymers127,6384
Non-polymers1,35718
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area19260 Å2
ΔGint-78 kcal/mol
Surface area33290 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5180 Å2
ΔGint-14 kcal/mol
Surface area21100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.000, 89.400, 78.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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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)
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 323 / 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: 2.2 Å3/Da / Density % sol: 44.07 %
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, PH 8.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Aug 14, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. all: 45083 / Num. obs: 44593 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.1 % / Biso Wilson estimate: 22.19 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 16.71
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.436 / Mean I/σ(I) obs: 2.4 / Num. unique all: 3248 / % possible all: 91.4

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Processing

Software
NameVersionClassification
StructureStudiodata collection
PHASERphasing
REFMAC5.5.0104refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3grk modified with ccp4 program chainsaw

3grk


Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.94 / SU B: 5.446 / SU ML: 0.071 / Isotropic thermal model: isotropic, TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.12 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.194 2251 5 %RANDOM
Rwork0.151 ---
all0.154 44593 --
obs0.154 44593 98.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.68 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å2-0 Å2-0 Å2
2--0.23 Å20 Å2
3----0.35 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3839 0 44 323 4206
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0223965
X-RAY DIFFRACTIONr_bond_other_d0.0010.022538
X-RAY DIFFRACTIONr_angle_refined_deg1.6731.9635381
X-RAY DIFFRACTIONr_angle_other_deg0.97636239
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7345523
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.67224.583144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.35115622
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9111511
X-RAY DIFFRACTIONr_chiral_restr0.0980.2633
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024431
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02770
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_it0.9561.52565
X-RAY DIFFRACTIONr_mcbond_other0.2791.51072
X-RAY DIFFRACTIONr_mcangle_it1.66324098
X-RAY DIFFRACTIONr_scbond_it2.69931400
X-RAY DIFFRACTIONr_scangle_it4.2324.51279
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 155 -
Rwork0.254 2813 -
obs--91.41 %
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)
10.1846-0.1032-0.01620.140.03540.27930.03730.02520.0348-0.0432-0.0275-0.0241-0.0341-0.0104-0.00990.02640.0038-0.00260.00820.01120.020736.658314.874563.9395
20.124-0.110.00130.1946-0.00720.2169-0.0306-0.0399-0.00080.03470.0340.0262-0.0216-0.0331-0.00350.01090.01520.00070.0323-0.01130.015928.92279.696794.3377
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999

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