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- PDB-6b9u: Crystal structure of 3-ketoacyl-(acyl-carrier-protein) reductase ... -

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Basic information

Entry
Database: PDB / ID: 6b9u
TitleCrystal structure of 3-ketoacyl-(acyl-carrier-protein) reductase from Brucella melitensis complexed with NADH
ComponentsDNA gyrase, subunit B:Short-chain dehydrogenase/reductase SDR:Glucose/ribitol dehydrogenase
KeywordsOXIDOREDUCTASE / 3-ketoacyl-(acyl-carrier-protein) reductase / Brucella melitensis / Seattle Structural Genomics Center for Infectious Disease / SSGCID / Structural Genomics
Function / homologyEnoyl-(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 / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / DNA gyrase, subunit B:Short-chain dehydrogenase/reductase SDR:Glucose/ribitol dehydrogenase
Function and homology information
Biological speciesBrucella abortus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To Be Published
Title: Crystal structure of 3-ketoacyl-(acyl-carrier-protein) reductase from Brucella melitensis complexed with NADH
Authors: Pierce, P.G. / Phan, J.N. / Lorimer, D.D. / Edwards, T.E.
History
DepositionOct 11, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA gyrase, subunit B:Short-chain dehydrogenase/reductase SDR:Glucose/ribitol dehydrogenase
B: DNA gyrase, subunit B:Short-chain dehydrogenase/reductase SDR:Glucose/ribitol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9754
Polymers53,6442
Non-polymers1,3312
Water6,017334
1
A: DNA gyrase, subunit B:Short-chain dehydrogenase/reductase SDR:Glucose/ribitol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4872
Polymers26,8221
Non-polymers6651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA gyrase, subunit B:Short-chain dehydrogenase/reductase SDR:Glucose/ribitol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4872
Polymers26,8221
Non-polymers6651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.130, 88.130, 111.950
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein DNA gyrase, subunit B:Short-chain dehydrogenase/reductase SDR:Glucose/ribitol dehydrogenase /


Mass: 26821.867 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella abortus (bacteria) / Strain: 2308 / Gene: BAB2_0975 / Plasmid: BrabA.00010.g.A1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2YJS1
#2: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH / Nicotinamide adenine dinucleotide


Mass: 665.441 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 334 / 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: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: BrabA.00010.g.A1.PS00350 at 20.22 mg/mL with 4 mM NAD was mixed 1:1 with Morpheus (b8): 12.5% (w/v) PEG1000, 12.5% (w/v) PEG3350, 12.5% (v/v) MPD, 0.1 M MOPS/HEPES-Na pH 7.5, 0.03 M NaF, 0. ...Details: BrabA.00010.g.A1.PS00350 at 20.22 mg/mL with 4 mM NAD was mixed 1:1 with Morpheus (b8): 12.5% (w/v) PEG1000, 12.5% (w/v) PEG3350, 12.5% (v/v) MPD, 0.1 M MOPS/HEPES-Na pH 7.5, 0.03 M NaF, 0.03 M NaBr, 0.03 M NaI. Crystal was harvested direct from tray 271654b8 into puck mkn8-10.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Mar 22, 2017
RadiationMonochromator: DIAMOND [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.8→41.643 Å / Num. obs: 40952 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 7.45 % / Biso Wilson estimate: 24.8 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.045 / Rrim(I) all: 0.048 / Χ2: 1.026 / Net I/σ(I): 26.72 / Num. measured all: 305083 / Scaling rejects: 7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.8-1.857.6150.513.5929240.9150.54797.6
1.85-1.97.590.3824.8228860.950.4197.8
1.9-1.957.5920.2796.6628220.9730.29998
1.95-2.017.5630.2278.2327210.9810.24498.2
2.01-2.087.5710.17610.6126540.9890.18998.2
2.08-2.157.5510.14313.2325810.9920.15398.4
2.15-2.237.5440.10617.5524780.9960.11398.5
2.23-2.327.4980.08820.9224200.9970.09598.8
2.32-2.437.50.07524.0823120.9980.08198.8
2.43-2.557.4980.06528.0922250.9980.0798.8
2.55-2.687.4590.05532.0221200.9990.05999.3
2.68-2.857.4420.04737.6320250.9990.0599.2
2.85-3.047.3920.0443.2919010.9990.04399.2
3.04-3.297.3640.03349.5817810.9990.03699.4
3.29-3.67.3240.02857.3516420.9990.0399.6
3.6-4.037.2690.02561.3815160.9990.02799.5
4.03-4.657.2110.02364.9713440.9990.02599.8
4.65-5.697.0790.0246511480.9990.02599.7
5.69-8.056.8760.0236291710.02599.3
8.05-41.6436.0540.02362.185350.9990.02596.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXdev_2499refinement
PDB_EXTRACT3.22data extraction
MoRDaphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3N74

3n74


Resolution: 1.8→41.643 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.49
RfactorNum. reflection% reflection
Rfree0.1995 2076 5.07 %
Rwork0.1596 --
obs0.1616 40945 98.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 88.45 Å2 / Biso mean: 30.0632 Å2 / Biso min: 12.24 Å2
Refinement stepCycle: final / Resolution: 1.8→41.643 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3441 0 88 334 3863
Biso mean--33.47 37.36 -
Num. residues----486
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053614
X-RAY DIFFRACTIONf_angle_d0.8384933
X-RAY DIFFRACTIONf_chiral_restr0.055591
X-RAY DIFFRACTIONf_plane_restr0.006635
X-RAY DIFFRACTIONf_dihedral_angle_d15.2442144
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.84190.32311420.23132501264398
1.8419-1.88790.24841330.19852522265598
1.8879-1.9390.25441360.17692517265398
1.939-1.9960.19371410.16792527266898
1.996-2.06040.21871370.16552553269098
2.0604-2.13410.23641220.16652562268499
2.1341-2.21950.21371340.15932563269799
2.2195-2.32050.20611360.15692583271999
2.3205-2.44290.19011120.1652597270999
2.4429-2.59590.23721200.16592617273799
2.5959-2.79630.21911470.17212590273799
2.7963-3.07760.2051570.16992592274999
3.0776-3.52270.20111520.15222641279399
3.5227-4.43750.14211490.135226932842100
4.4375-41.65370.19511580.15632811296999
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)
11.21220.465-0.28340.8041-0.04510.6430.06650.14650.28390.05140.10620.4394-0.0234-0.238-0.17710.18060.02530.03420.25840.11690.4085-27.64452.6135-27.1616
21.89560.8006-1.8412.7255-3.12589.1321-0.01140.0520.15520.04990.13660.30220.0706-0.0588-0.0990.10920.02770.03150.11040.02780.2478-12.99823.1788-26.8227
32.4234-0.13060.04823.03951.2181.88170.09570.52720.1957-0.44780.05650.3386-0.1705-0.2407-0.13650.20050.0166-0.04060.26380.07810.238-14.7844-6.6725-34.304
41.3350.5181-0.10711.486-0.08160.94840.00140.011-0.1915-0.02510.0290.0050.1377-0.0362-0.03330.18650.0199-0.01270.15440.01070.14783.2773-24.379-26.7854
52.4009-0.2755-1.32883.303-0.26720.864-0.0442-0.4036-0.04870.54640.1107-0.04790.16910.1563-0.08580.21720.0287-0.00020.20810.03530.1739-5.2891-14.3336-20.0002
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 133 )A3 - 133
2X-RAY DIFFRACTION2chain 'A' and (resid 134 through 178 )A134 - 178
3X-RAY DIFFRACTION3chain 'A' and (resid 179 through 253 )A179 - 253
4X-RAY DIFFRACTION4chain 'B' and (resid 3 through 178 )B3 - 178
5X-RAY DIFFRACTION5chain 'B' and (resid 179 through 253 )B179 - 253

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