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- PDB-4nbr: Crystal Structure of 3-oxoacyl-[acyl-carrier protein] reductase f... -

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Basic information

Entry
Database: PDB / ID: 4nbr
TitleCrystal Structure of 3-oxoacyl-[acyl-carrier protein] reductase from Brucella melitensis ATCC 23457
ComponentsHypothetical 3-oxoacyl-(Acyl-carrier protein) reductase
KeywordsOXIDOREDUCTASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID / short chain dehydrogenase
Function / homology
Function and homology information


oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
Similarity search - Function
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
Hypothetical 3-oxoacyl-(Acyl-carrier protein) reductase
Similarity search - Component
Biological speciesBrucella abortus bv. 1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.35 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: TO BE PUBLISHED
Title: Crystal Structure of 3-oxoacyl-[acyl-carrier protein] reductase from Brucella melitensis ATCC 23457
Authors: Dranow, D.M. / Abendroth, J. / Edwards, T.E. / Lorimer, D.
History
DepositionOct 23, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 10, 2014Group: Structure summary
Revision 1.2Dec 17, 2014Group: Data collection
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Revision 1.4Sep 20, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypothetical 3-oxoacyl-(Acyl-carrier protein) reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2022
Polymers29,1101
Non-polymers921
Water5,945330
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Hypothetical 3-oxoacyl-(Acyl-carrier protein) reductase
hetero molecules

A: Hypothetical 3-oxoacyl-(Acyl-carrier protein) reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,4054
Polymers58,2202
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area4730 Å2
ΔGint-30 kcal/mol
Surface area21330 Å2
MethodPISA
3
A: Hypothetical 3-oxoacyl-(Acyl-carrier protein) reductase
hetero molecules

A: Hypothetical 3-oxoacyl-(Acyl-carrier protein) reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,4054
Polymers58,2202
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area4080 Å2
ΔGint-29 kcal/mol
Surface area21990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.760, 76.620, 87.600
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-489-

HOH

21A-629-

HOH

31A-654-

HOH

41A-655-

HOH

51A-722-

HOH

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Components

#1: Protein Hypothetical 3-oxoacyl-(Acyl-carrier protein) reductase


Mass: 29110.240 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella abortus bv. 1 (bacteria) / Strain: ATCC 23457 / Gene: BruAb2_0805 / Production host: Escherichia coli (E. coli) / References: UniProt: Q577I6
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 330 / 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: 2.07 Å3/Da / Density % sol: 40.53 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: JCSG+(e1): 1M Sodium Citrate Tribasic, 0.1M Sodium Cacodylate/HCl, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 16, 2013 / Details: Beryllium Lenses
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.35→50 Å / Num. all: 53242 / Num. obs: 53190 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Biso Wilson estimate: 18.05 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 19.27
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.35-1.390.4522.9115483387399.9
1.39-1.420.3834.0820296381499.9
1.42-1.460.3375.06221403654100
1.46-1.510.256.74218513601100
1.51-1.560.1918.7221169348599.9
1.56-1.610.179.88206323373100
1.61-1.670.13512198903254100
1.67-1.740.11414.2919231313499.9
1.74-1.820.09516.9618498301799.9
1.82-1.910.07520.59179252909100
1.91-2.010.06124.77169252748100
2.01-2.130.05229.36160442604100
2.13-2.280.04532.67150642447100
2.28-2.460.04235.8614028228499.9
2.46-2.70.0438.0812905210299.9
2.7-3.020.03741.6211775192499.9
3.02-3.490.03444.7110402170799.8
3.49-4.270.03247.648861146599.9
4.27-6.040.03247.566723113999.8
6.040.03445.99353465696.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.5phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SJ7

3sj7


Resolution: 1.35→50 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.975 / WRfactor Rfree: 0.1286 / WRfactor Rwork: 0.0981 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.9235 / SU B: 1.341 / SU ML: 0.024 / SU R Cruickshank DPI: 0.0398 / SU Rfree: 0.0399 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.04 / ESU R Free: 0.04 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1332 2702 5.1 %RANDOM
Rwork0.1004 ---
all0.102 55891 --
obs0.102 53189 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 71.3 Å2 / Biso mean: 15.711 Å2 / Biso min: 4.28 Å2
Baniso -1Baniso -2Baniso -3
1--0.4 Å20 Å2-0 Å2
2---0.13 Å20 Å2
3---0.53 Å2
Refinement stepCycle: LAST / Resolution: 1.35→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1977 0 6 330 2313
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0192127
X-RAY DIFFRACTIONr_bond_other_d0.0010.022064
X-RAY DIFFRACTIONr_angle_refined_deg1.4731.9552931
X-RAY DIFFRACTIONr_angle_other_deg0.84834745
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9175301
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.33123.48886
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.84915335
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5631517
X-RAY DIFFRACTIONr_chiral_restr0.0920.2353
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212473
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02472
X-RAY DIFFRACTIONr_mcbond_it1.5051.1711105
X-RAY DIFFRACTIONr_mcbond_other1.5051.171104
X-RAY DIFFRACTIONr_mcangle_it1.8461.771388
X-RAY DIFFRACTIONr_rigid_bond_restr2.6734190
X-RAY DIFFRACTIONr_sphericity_free31.768570
X-RAY DIFFRACTIONr_sphericity_bonded8.45354397
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.225 177 -
Rwork0.179 3693 -
all-3870 -
obs--99.87 %

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