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- PDB-4zju: Structure of a NADH-dependent enoyl-ACP reductase from Acinetobac... -

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Basic information

Entry
Database: PDB / ID: 4zju
TitleStructure of a NADH-dependent enoyl-ACP reductase from Acinetobacter baumannii in complex with NAD
ComponentsEnoyl-[acyl-carrier-protein] reductase [NADH]
KeywordsOXIDOREDUCTASE / SSGCID / NADH-dependent enoyl-ACP reductase / NAD / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homologyenoyl-[acyl-carrier-protein] reductase (NADH) / NAD(P)-binding Rossmann-like Domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Enoyl-[acyl-carrier-protein] reductase [NADH] / Enoyl-[acyl-carrier-protein] reductase [NADH]
Function and homology information
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.2 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Structure of a NADH-dependent enoyl-ACP reductase from Acinetobacter baumannii in complex with NAD
Authors: Abendroth, J. / Lorimer, D.D. / Edwards, T.E.
History
DepositionApr 29, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_keywords
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr2_auth_seq_id / _struct_keywords.text

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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]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3783
Polymers29,6921
Non-polymers6862
Water7,008389
1
A: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules

A: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules

A: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules

A: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,51312
Polymers118,7684
Non-polymers2,7468
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area19430 Å2
ΔGint-164 kcal/mol
Surface area34030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.020, 92.440, 93.830
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-486-

HOH

21A-591-

HOH

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Components

#1: Protein Enoyl-[acyl-carrier-protein] reductase [NADH]


Mass: 29691.902 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: fabI, IOMTU433_3282 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: V5VH25, UniProt: A0A7U4SQ27*PLUS, 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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 389 / 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: 2.6 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Molecular Dimensions Morpheus screen, h12: Morpheus H12: 20mM each L-Na-Glutamate, Alanine (racemic), Glycine, Lysine HCl (racemic), Serine (racemic); 100mM Tris (base)/Bicine pH 8.5; 15% ...Details: Molecular Dimensions Morpheus screen, h12: Morpheus H12: 20mM each L-Na-Glutamate, Alanine (racemic), Glycine, Lysine HCl (racemic), Serine (racemic); 100mM Tris (base)/Bicine pH 8.5; 15% each MPD (racemic), PEG 1000, PEG 3350; AcbaC.00170.a.B1.PW37673 at 25mg/ml with 5mM NADH; tray 262582, puck oxi7-1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Apr 9, 2015
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.2→50 Å / Num. obs: 96282 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Biso Wilson estimate: 9.45 Å2 / Rmerge F obs: 1 / Rmerge(I) obs: 0.049 / Rrim(I) all: 0.055 / Χ2: 1.018 / Net I/σ(I): 18.71 / Num. measured all: 463957
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.2-1.234.60.8150.5372.7532123705670530.607100
1.23-1.260.8620.473.2832920690969080.528100
1.26-1.30.8930.3963.931804664666460.445100
1.3-1.340.9240.3394.5231412654765450.381100
1.34-1.390.950.2875.4230505631863170.322100
1.39-1.430.9620.2296.8429517610361010.257100
1.43-1.490.9730.1888.2428530588158790.211100
1.49-1.550.9860.14410.4927770570157010.162100
1.55-1.620.990.11113.5726588545054500.125100
1.62-1.70.9930.09416.1225546521252120.106100
1.7-1.790.9950.07420.224356498049780.083100
1.79-1.90.9970.0582523022469146890.065100
1.9-2.030.9980.04631.4121824446844630.05199.9
2.03-2.190.9990.03637.3420095411941190.041100
2.19-2.40.9990.03242.1718737384038380.03699.9
2.4-2.680.9990.02648.0316816346734650.0399.9
2.68-3.10.9990.02353.7414932307830770.025100
3.1-3.790.9990.01959.7212550261726120.02299.8
3.79-5.3710.01762.769784206520640.02100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
ARP3.15model building
Cootmodel building
PDB_EXTRACTdata extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4NQZ

4nqz


Resolution: 1.2→46.915 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 12.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.142 2015 2.09 %Random selection
Rwork0.1248 94262 --
obs0.1252 96277 99.94 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 61.16 Å2 / Biso mean: 15.1289 Å2 / Biso min: 6.4 Å2
Refinement stepCycle: final / Resolution: 1.2→46.915 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1941 0 45 405 2391
Biso mean--9.53 29.76 -
Num. residues----260
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062138
X-RAY DIFFRACTIONf_angle_d1.2692925
X-RAY DIFFRACTIONf_chiral_restr0.072333
X-RAY DIFFRACTIONf_plane_restr0.006376
X-RAY DIFFRACTIONf_dihedral_angle_d12.665786
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.2-1.230.21851440.183566726816
1.23-1.26330.19751340.163666746808
1.2633-1.30040.1821420.148566546796
1.3004-1.34240.14251460.138166916837
1.3424-1.39040.16181440.128866706814
1.3904-1.44610.12691410.113767096850
1.4461-1.51190.1361450.107166976842
1.5119-1.59160.11641410.102467286869
1.5916-1.69130.1391460.103767116857
1.6913-1.82190.12661430.110267256868
1.8219-2.00530.13351400.111367366876
2.0053-2.29540.12071490.116867576906
2.2954-2.8920.15661450.131468246969
2.892-46.95090.13931550.131870147169

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