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- PDB-5ts3: Crystal Structure of a 3-oxoacyl-[acyl-carrier protein] Reductase... -

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Basic information

Entry
Database: PDB / ID: 5ts3
TitleCrystal Structure of a 3-oxoacyl-[acyl-carrier protein] Reductase with bound NAD from Brucella melitensis
ComponentsShort-chain dehydrogenase/reductase SDR
KeywordsOXIDOREDUCTASE / SSGCID / Brucella melitensis / NAD / 3-oxoacyl-[acyl-carrier protein] reductase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


oxidoreductase activity / nucleotide binding
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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Short-chain dehydrogenase/reductase SDR
Similarity search - Component
Biological speciesBrucella melitensis biotype 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.55 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of a 3-oxoacyl-[acyl-carrier protein] Reductase with bound NAD from Brucella melitensis
Authors: Dranow, D.M. / Lorimer, D.D. / Edwards, T.E.
History
DepositionOct 27, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software / Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Oct 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

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Assembly

Deposited unit
A: Short-chain dehydrogenase/reductase SDR
B: Short-chain dehydrogenase/reductase SDR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,53017
Polymers58,2202
Non-polymers2,31015
Water10,034557
1
A: Short-chain dehydrogenase/reductase SDR
B: Short-chain dehydrogenase/reductase SDR
hetero molecules

A: Short-chain dehydrogenase/reductase SDR
B: Short-chain dehydrogenase/reductase SDR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,06134
Polymers116,4414
Non-polymers4,62030
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area24550 Å2
ΔGint-82 kcal/mol
Surface area32300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.070, 105.620, 126.040
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-561-

HOH

21A-616-

HOH

31B-575-

HOH

41B-586-

HOH

51B-612-

HOH

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Components

#1: Protein Short-chain dehydrogenase/reductase SDR


Mass: 29110.240 Da / Num. of mol.: 2 / Fragment: BrmeB.00010.f.B1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella melitensis biotype 2 (strain ATCC 23457) (bacteria)
Strain: ATCC 23457 / Gene: BMEA_B0375 / Plasmid: BrmeB.00010.f.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C0RKU3
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 557 / 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: 2.37 Å3/Da / Density % sol: 48.19 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: BrmeB.00010.f.B1.PS01889 at 17.41 mg/ml, incubated with 4mM NAD, mixed 1:1 with an equal volume MCSG1(a1): 20% (w/v) PEG-8000, 0.1 M HEPES/NaOH, pH=7.5, cryoprotected with 20% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 20, 2016 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.55→35 Å / Num. obs: 79835 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 12.72 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.073 / Rrim(I) all: 0.081 / Χ2: 0.961 / Net I/σ(I): 14.53 / Num. measured all: 393292
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
1.55-1.594.50.5242.930.829198.1
1.59-1.630.4733.520.868198.9
1.63-1.680.3874.260.917198.9
1.68-1.730.3075.270.94199.3
1.73-1.790.2646.180.958199.4
1.79-1.850.217.640.973199.4
1.85-1.920.1619.830.983199.5
1.92-20.13111.720.989199.4
2-2.090.10314.150.992199.5
2.09-2.190.08416.670.995199.6
2.19-2.310.07318.810.996199.5
2.31-2.450.06420.710.997199.7
2.45-2.620.05922.650.997199.6
2.62-2.830.05124.910.997199.6
2.83-3.10.04528.150.997199.6
3.1-3.470.04230.990.998199.7
3.47-40.03933.70.998199.7
4-4.90.03634.740.998199.7
4.9-6.930.03733.650.998199.9
6.93-350.03734.580.998195.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.2data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NBR

4nbr


Resolution: 1.55→34.68 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.69
RfactorNum. reflection% reflection
Rfree0.1695 1906 2.39 %
Rwork0.1461 --
obs0.1466 79815 99.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 69.81 Å2 / Biso mean: 17.6239 Å2 / Biso min: 5.36 Å2
Refinement stepCycle: final / Resolution: 1.55→34.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3860 0 163 570 4593
Biso mean--23.67 30.5 -
Num. residues----527
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064172
X-RAY DIFFRACTIONf_angle_d0.8145703
X-RAY DIFFRACTIONf_chiral_restr0.054680
X-RAY DIFFRACTIONf_plane_restr0.006769
X-RAY DIFFRACTIONf_dihedral_angle_d11.4262534
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.55-1.58880.21931390.19265444558398
1.5888-1.63180.23821350.18795499563499
1.6318-1.67980.22741270.185526565399
1.6798-1.7340.22311280.16565481560999
1.734-1.7960.16671250.16145520564599
1.796-1.86790.19911380.158555685706100
1.8679-1.95290.17791410.15025500564199
1.9529-2.05580.1721490.148455495698100
2.0558-2.18460.15311220.135755865708100
2.1846-2.35320.14821340.13795555568999
2.3532-2.590.15791380.138756295767100
2.59-2.96460.15151350.141556025737100
2.9646-3.73440.17461630.136456515814100
3.7344-34.68890.14871320.1375799593199
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)
12.4109-0.54620.06821.0318-0.1484.81840.14770.2674-0.101-0.1618-0.1114-0.13690.0740.8292-0.13020.13060.02590.00120.19170.02090.1831-16.5539-6.729-1.6012
20.9746-0.15370.17661.2559-0.31771.79870.0048-0.0489-0.23790.0066-0.0109-0.11460.17120.1677-0.00310.0790.0272-0.01120.10050.01190.1328-20.5903-17.886310.4073
35.4541.3186-2.78291.2971-0.84953.13890.1184-0.3324-0.24040.1702-0.1477-0.24450.09720.31420.02810.09480.0307-0.0250.1120.0220.128-23.0164-17.875517.3534
41.49610.55290.33160.91480.17870.74850.0079-0.0214-0.14370.03190.0083-0.01510.10830.0428-0.03570.09250.0135-0.00020.06510.00780.0701-37.3122-16.451815.7991
53.47481.66841.53582.28621.37792.5764-0.07420.15540.0037-0.04070.04430.0402-0.01340.0886-0.01440.07340.00420.01560.05820.00490.0518-37.5577-9.35585.4541
61.31821.42110.64332.88561.19881.0601-0.0190.0117-0.0113-0.01970.01780.0192-0.0149-0.0021-0.00660.08510.00120.00690.08630.00830.0683-40.6156-5.237611.94
71.1741-0.2891-0.47960.5456-0.51361.04060.16320.0497-0.3053-0.0755-0.1255-0.10490.2411-0.21090.01070.09870.0008-0.03460.0806-0.00470.1213-33.3397-12.91321.7292
80.674-0.30110.24731.07230.59672.11560.03970.0471-0.1822-0.0304-0.04020.0730.21430.03380.00330.11430.01230.0020.0822-0.00470.1214-31.4264-13.1161-6.2683
90.7136-0.12080.25631.42490.84512.12410.0031-0.01310.01770.0314-0.08780.09010.0341-0.07850.08450.0749-0.00220.00840.06140.00450.0736-33.4611-1.81680.6129
101.4876-0.1699-0.1081.9583-0.77521.40450.0065-0.16820.09840.22220.13350.351-0.1124-0.2893-0.05710.1141-0.00120.04940.2145-0.00560.2051-73.4093-4.449114.8427
110.47580.04570.32560.56510.16160.77940.0103-0.0654-0.07310.05630.00040.08950.088-0.1104-0.00470.0855-0.0160.01260.08530.00380.0892-56.3571-12.122314.5817
120.91770.4120.25892.27670.43190.92010.0382-0.07880.03510.2024-0.0290.0643-0.0191-0.07160.00130.08060.00450.00520.0916-0.00410.076-61.10532.05868.1216
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 20 )A1 - 20
2X-RAY DIFFRACTION2chain 'A' and (resid 21 through 66 )A21 - 66
3X-RAY DIFFRACTION3chain 'A' and (resid 67 through 80 )A67 - 80
4X-RAY DIFFRACTION4chain 'A' and (resid 81 through 148 )A81 - 148
5X-RAY DIFFRACTION5chain 'A' and (resid 149 through 169 )A149 - 169
6X-RAY DIFFRACTION6chain 'A' and (resid 170 through 193 )A170 - 193
7X-RAY DIFFRACTION7chain 'A' and (resid 194 through 214 )A194 - 214
8X-RAY DIFFRACTION8chain 'A' and (resid 215 through 244 )A215 - 244
9X-RAY DIFFRACTION9chain 'A' and (resid 245 through 265 )A245 - 265
10X-RAY DIFFRACTION10chain 'B' and (resid -2 through 66 )B-2 - 66
11X-RAY DIFFRACTION11chain 'B' and (resid 67 through 193 )B67 - 193
12X-RAY DIFFRACTION12chain 'B' and (resid 194 through 265 )B194 - 265

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