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- PDB-4o5o: X-ray Crystal Structure of a 3-hydroxyacyl-CoA dehydrogenase from... -

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Basic information

Entry
Database: PDB / ID: 4o5o
TitleX-ray Crystal Structure of a 3-hydroxyacyl-CoA dehydrogenase from Brucella suis
Components3-hydroxyacyl-CoA dehydrogenase
KeywordsOXIDOREDUCTASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


oxidoreductase activity / metal ion binding
Similarity search - Function
short chain dehydrogenase / PKS_KR / 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
3-hydroxyacyl-CoA dehydrogenase, putative / 3-hydroxyacyl-CoA dehydrogenase, putative
Similarity search - Component
Biological speciesBrucella suis ("Organism resembling Bacillus abortus" Traum 1914)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: TO BE PUBLISHED
Title: X-ray Crystal Structure of a 3-hydroxyacyl-CoA dehydrogenase from Brucella suis
Authors: Fairman, J.W. / Abendroth, J. / Edwards, T.E. / Lorimer, D.
History
DepositionDec 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 1, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _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: 3-hydroxyacyl-CoA dehydrogenase
B: 3-hydroxyacyl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8586
Polymers54,5472
Non-polymers3124
Water10,827601
1
A: 3-hydroxyacyl-CoA dehydrogenase
B: 3-hydroxyacyl-CoA dehydrogenase
hetero molecules

A: 3-hydroxyacyl-CoA dehydrogenase
B: 3-hydroxyacyl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,71712
Polymers109,0944
Non-polymers6238
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area16350 Å2
ΔGint-183 kcal/mol
Surface area33720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.470, 92.240, 135.490
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-601-

HOH

21B-544-

HOH

31B-668-

HOH

DetailsAS PER THE AUTHORS THE BIOLOGICAL ASSEMBLY IS UNKNOWN

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Components

#1: Protein 3-hydroxyacyl-CoA dehydrogenase


Mass: 27273.404 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella suis ("Organism resembling Bacillus abortus" Traum 1914)
Strain: 1330 / Gene: BRA0449, BS1330_II0446 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8FWK3, UniProt: A0A0H3G6B0*PLUS
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 601 / 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: 2.19 Å3/Da / Density % sol: 43.84 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.4 uL protein at 19.86 mg/mL + 0.4 uL JCSG+ D5 - 0.1 M HEPES pH 7.50, 70% MPD, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Sep 25, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. all: 94147 / Num. obs: 92937 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 16.899 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 47.68
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.4-1.440.4615.3170148643393.4
1.44-1.480.318.175047634394.6
1.48-1.520.3028.983501632396.5
1.52-1.570.22912.64101969634999.7
1.57-1.620.18616.851260966173100
1.62-1.670.15719.791287505989100
1.67-1.740.12924.241291805748100
1.74-1.810.10929.081310985574100
1.81-1.890.10932.13130247529999.6
1.89-1.980.12441.62115038500198.3
1.98-2.090.0655.341302494869100
2.09-2.210.05665.64127515462099.8
2.21-2.370.06374.85102524430099.4
2.37-2.560.03885.251165784058100
2.56-2.80.03494.671096683716100
2.8-3.130.03108.051036503400100
3.13-3.610.028128.78990393007100
3.61-4.430.027149.2789681255199.9
4.43-6.260.022176.51987152019100
6.260.023191.0161424116599.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMAC5.8.0049refinement
PDB_EXTRACT3.14data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→38.235 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.958 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 1.543 / SU ML: 0.031 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.056 / ESU R Free: 0.053 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1687 4661 5 %RANDOM
Rwork0.1356 ---
obs0.1373 92937 98.71 %-
all-94147 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 69.15 Å2 / Biso mean: 13.6246 Å2 / Biso min: 4.02 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å2-0 Å2
2--0.23 Å20 Å2
3----0.29 Å2
Refinement stepCycle: LAST / Resolution: 1.4→38.235 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3677 0 17 601 4295
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0193788
X-RAY DIFFRACTIONr_bond_other_d0.0010.023751
X-RAY DIFFRACTIONr_angle_refined_deg1.4431.9625139
X-RAY DIFFRACTIONr_angle_other_deg0.79938559
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8725529
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.14323.406138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.53715584
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9421527
X-RAY DIFFRACTIONr_chiral_restr0.0880.2606
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214416
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02833
X-RAY DIFFRACTIONr_mcbond_it1.571.0432085
X-RAY DIFFRACTIONr_mcbond_other1.5721.5762082
X-RAY DIFFRACTIONr_mcangle_it1.9141.5692602
X-RAY DIFFRACTIONr_rigid_bond_restr2.26733760
X-RAY DIFFRACTIONr_sphericity_bonded10.62853700
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.212 334 -
Rwork0.162 6091 -
all-6425 -
obs--93.39 %

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