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- PDB-4xgn: Crystal structure of 3-hydroxyacyl-CoA dehydrogenase in complex w... -

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Basic information

Entry
Database: PDB / ID: 4xgn
TitleCrystal structure of 3-hydroxyacyl-CoA dehydrogenase in complex with NAD from Burkholderia thailandensis
Components3-hydroxyacyl-CoA dehydrogenase
KeywordsOXIDOREDUCTASE / SSGCID / 3-hydroxyacyl-CoA dehydrogenase / Burkholderia thailandensis / 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 / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / 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 / 3-hydroxyacyl-CoA dehydrogenase
Similarity search - Component
Biological speciesBurkholderia thailandensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of 3-hydroxyacyl-CoA dehydrogenase in complex with NAD from Burkholderia thailandensis
Authors: Abendroth, J. / Dranow, D.M. / Lorimer, D.D. / Edwards, T.E.
History
DepositionDec 31, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 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_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / 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_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3-hydroxyacyl-CoA dehydrogenase
B: 3-hydroxyacyl-CoA dehydrogenase
C: 3-hydroxyacyl-CoA dehydrogenase
D: 3-hydroxyacyl-CoA dehydrogenase
E: 3-hydroxyacyl-CoA dehydrogenase
F: 3-hydroxyacyl-CoA dehydrogenase
G: 3-hydroxyacyl-CoA dehydrogenase
H: 3-hydroxyacyl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)223,06635
Polymers216,4598
Non-polymers6,60727
Water34,6431923
1
A: 3-hydroxyacyl-CoA dehydrogenase
B: 3-hydroxyacyl-CoA dehydrogenase
C: 3-hydroxyacyl-CoA dehydrogenase
D: 3-hydroxyacyl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,50217
Polymers108,2294
Non-polymers3,27213
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20840 Å2
ΔGint-118 kcal/mol
Surface area30750 Å2
MethodPISA
2
E: 3-hydroxyacyl-CoA dehydrogenase
F: 3-hydroxyacyl-CoA dehydrogenase
G: 3-hydroxyacyl-CoA dehydrogenase
H: 3-hydroxyacyl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,56418
Polymers108,2294
Non-polymers3,33414
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21070 Å2
ΔGint-115 kcal/mol
Surface area30240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.220, 77.100, 109.350
Angle α, β, γ (deg.)103.260, 93.980, 109.680
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
3-hydroxyacyl-CoA dehydrogenase


Mass: 27057.359 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia thailandensis (bacteria) / Strain: E264 / ATCC 700388 / DSM 13276 / CIP 106301 / Gene: BTH_I0738 / Plasmid: ButhA.00010.l.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2T0K5
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 1923 / 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: 2.52 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Morpheus screen c6: 10% PEG 8000, 20% EG; 30mM each NaNO3, Na2HPO4, (NH4)2SO4; 100mM MOPS/HEPES pH 7.5; ButhA.0010.l.B1.PS01726 at 10mg/ml with 2.5mM NAD; direct cryo; tray 252631c6, puck sxz2-6

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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-225 / Detector: CCD / Date: Feb 12, 2014
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. all: 253404 / Num. obs: 246070 / % possible obs: 97.1 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 22.006 Å2 / Rmerge F obs: 0.996 / Rmerge(I) obs: 0.081 / Rrim(I) all: 0.094 / Χ2: 0.937 / Net I/σ(I): 11.23 / Num. measured all: 976151
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.65-1.6940.8950.4762.887128318769179030.5595.4
1.69-1.740.920.3863.456963718306174860.44695.5
1.74-1.790.9420.3244.046798817822170800.37595.8
1.79-1.840.9590.2614.926578517193165330.30296.2
1.84-1.910.9710.215.936405116717160970.24396.3
1.91-1.970.980.1727.066222816209156500.19996.6
1.97-2.050.9870.1398.436002715590151010.16196.9
2.05-2.130.990.1110.275773815001145370.12796.9
2.13-2.220.9920.09611.395572614405140190.11197.3
2.22-2.330.9940.08412.735330613769134240.09897.5
2.33-2.460.9940.07713.955090313112128150.08997.7
2.46-2.610.9950.06915.154814312376121180.0897.9
2.61-2.790.9950.06416.64522211605114020.07498.3
2.79-3.010.9950.0618.114235110867106940.0798.4
3.01-3.30.9950.05620.2738838997798370.06598.6
3.3-3.690.9950.05222.535108900788960.0698.8
3.69-4.260.9940.05323.7530936795878820.06199
4.26-5.220.9950.05224.5326148670266550.0699.3
5.22-7.380.9920.05823.6420081517351350.06799.3
7.380.9910.05925.1310652284628060.06998.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
ARPmodel building
Cootmodel building
REFMACrefinement
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TPC

3tpc


Resolution: 1.65→50 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.96 / WRfactor Rfree: 0.1762 / WRfactor Rwork: 0.1522 / FOM work R set: 0.8769 / SU B: 3.307 / SU ML: 0.056 / SU R Cruickshank DPI: 0.084 / SU Rfree: 0.0811 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.084 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1771 12256 5 %RANDOM
Rwork0.1545 233814 --
obs0.1557 233814 97.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 56.45 Å2 / Biso mean: 16.931 Å2 / Biso min: 7.11 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å2-0.56 Å20.22 Å2
2---0.19 Å2-0.01 Å2
3---0.23 Å2
Refinement stepCycle: final / Resolution: 1.65→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14506 0 468 1923 16897
Biso mean--14.73 29.36 -
Num. residues----2037
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01915381
X-RAY DIFFRACTIONr_bond_other_d0.0020.0215247
X-RAY DIFFRACTIONr_angle_refined_deg1.742.01320953
X-RAY DIFFRACTIONr_angle_other_deg0.98334893
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.99352088
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.29123.786523
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.797152356
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0815113
X-RAY DIFFRACTIONr_chiral_restr0.0950.22506
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02117492
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023207
X-RAY DIFFRACTIONr_mcbond_it0.6340.9258200
X-RAY DIFFRACTIONr_mcbond_other0.6330.9258199
X-RAY DIFFRACTIONr_mcangle_it1.1071.38310251
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.232 863 -
Rwork0.213 17015 -
all-17878 -
obs--95.35 %
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)
10.34650.228-0.17820.3944-0.06240.5934-0.04890.0322-0.00930.0051-0.0050.03750.159-0.08530.0540.1191-0.06180.06360.0325-0.03340.0391-41.335-155.608158.498
20.33370.1103-0.10770.47310.04010.50980.0239-0.00950.0327-0.01010.00530.0129-0.10120.0498-0.02920.0841-0.04890.03730.0311-0.01940.0218-19.123-121.201150.724
30.38360.1219-0.19020.3520.03170.56460.0686-0.07890.02940.0935-0.06870.01840.00880.09680.00010.1025-0.05490.04180.0496-0.02130.0186-27.105-134.911175.525
40.40540.0985-0.22470.4964-0.03490.6168-0.08210.0584-0.0565-0.08620.0391-0.02780.1028-0.00920.0430.0961-0.05070.04850.0339-0.02870.0265-24.247-146.927136.019
50.47150.1268-0.20640.35760.01190.5230.0654-0.07820.0530.0805-0.04030.0365-0.05350.0484-0.02510.1007-0.0540.04140.0337-0.02490.0188-65.885-114.306120.343
60.38770.108-0.20690.45160.08290.6096-0.0807-0.0126-0.0815-0.0530.0473-0.0760.08040.03730.03330.0951-0.0430.05550.0334-0.02420.0401-48.765-135.42288.888
70.40610.1351-0.08190.42790.09370.4108-0.03870.0338-0.04240.0243-0.01970.04020.0763-0.05420.05840.0939-0.05270.04670.0317-0.02660.0303-73.935-138.425103.814
80.4770.1119-0.27640.43190.04140.46730.0546-0.03960.0662-0.0410.0314-0.0217-0.10450.0611-0.0860.1058-0.06630.04840.0421-0.03060.0274-47.532-106.58698.561
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 301
2X-RAY DIFFRACTION2B-1 - 301
3X-RAY DIFFRACTION3C-2 - 301
4X-RAY DIFFRACTION4D-1 - 301
5X-RAY DIFFRACTION5E-2 - 301
6X-RAY DIFFRACTION6F-2 - 301
7X-RAY DIFFRACTION7G-2 - 301
8X-RAY DIFFRACTION8H-2 - 301

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