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- PDB-3icc: Crystal structure of a putative 3-oxoacyl-(acyl carrier protein) ... -

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Basic information

Entry
Database: PDB / ID: 3icc
TitleCrystal structure of a putative 3-oxoacyl-(acyl carrier protein) reductase from Bacillus anthracis at 1.87 A resolution
ComponentsPutative 3-oxoacyl-(acyl carrier protein) reductase
KeywordsOXIDOREDUCTASE / structural genomics / putative 3-oxoacyl-(acyl carrier protein) reductase / Center for Structural Genomics of Infectious Diseases / CSGID
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. / 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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 3-oxoacyl-acyl-carrier-protein reductase FabG / Oxidoreductase, short-chain dehydrogenase/reductase family
Similarity search - Component
Biological speciesBacillus anthracis str. 'Ames Ancestor' (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.87 Å
AuthorsHou, J. / Chruszcz, M. / Zheng, H. / Cymborowski, M. / Luo, H.-B. / Skarina, T. / Gordon, S. / Savchenko, A. / Edwards, A.M. / Anderson, W. ...Hou, J. / Chruszcz, M. / Zheng, H. / Cymborowski, M. / Luo, H.-B. / Skarina, T. / Gordon, S. / Savchenko, A. / Edwards, A.M. / Anderson, W. / Minor, W. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2012
Title: Structure of a short-chain dehydrogenase/reductase from Bacillus anthracis.
Authors: Hou, J. / Wojciechowska, K. / Zheng, H. / Chruszcz, M. / Cooper, D.R. / Cymborowski, M. / Skarina, T. / Gordon, E. / Luo, H. / Savchenko, A. / Minor, W.
History
DepositionJul 17, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jun 6, 2012Group: Database references
Revision 1.3Dec 26, 2012Group: Database references
Revision 1.4Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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: Putative 3-oxoacyl-(acyl carrier protein) reductase
B: Putative 3-oxoacyl-(acyl carrier protein) reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,37412
Polymers55,2622
Non-polymers2,11210
Water5,188288
1
A: Putative 3-oxoacyl-(acyl carrier protein) reductase
B: Putative 3-oxoacyl-(acyl carrier protein) reductase
hetero molecules

A: Putative 3-oxoacyl-(acyl carrier protein) reductase
B: Putative 3-oxoacyl-(acyl carrier protein) reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,74924
Polymers110,5254
Non-polymers4,22420
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area12750 Å2
ΔGint-107.1 kcal/mol
Surface area36530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.734, 104.835, 103.684
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Putative 3-oxoacyl-(acyl carrier protein) reductase


Mass: 27631.164 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis str. 'Ames Ancestor' (bacteria)
Strain: Ames Ancestor / Gene: BAS1712, BA_1847, GBAA1847, GBAA_1847 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL / References: UniProt: Q81S30, UniProt: A0A6L7HAY4*PLUS

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Non-polymers , 5 types, 298 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 288 / 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: 2.43 Å3/Da / Density % sol: 49.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 30% PEG MME 5000, 0.2M Ammonium sulfate, 0.1M MES pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 14, 2009 / Details: Mirrors
RadiationMonochromator: Si(111) channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.87→50 Å / Num. all: 44201 / Num. obs: 44201 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 21.3 Å2 / Rmerge(I) obs: 0.1 / Rsym value: 0.1 / Net I/σ(I): 46.3
Reflection shellResolution: 1.87→1.9 Å / Redundancy: 7 % / Rmerge(I) obs: 0.686 / Mean I/σ(I) obs: 3 / Num. unique all: 2186 / Rsym value: 0.686 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-3000data collection
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
MLPHAREphasing
DMmodel building
CCP4model building
SOLVEphasing
RESOLVEmodel building
ARP/wARPmodel building
Cootmodel building
REFMAC5.5.0072refinement
HKL-2000data reduction
HKL-2000data scaling
DMphasing
CCP4phasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.87→50 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.939 / SU B: 5.632 / SU ML: 0.078 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.132 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20676 2227 5 %RANDOM
Rwork0.16615 ---
all0.16817 41930 --
obs0.16817 41930 98.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 13.376 Å2
Baniso -1Baniso -2Baniso -3
1-3.43 Å20 Å20 Å2
2---1.77 Å20 Å2
3----1.66 Å2
Refinement stepCycle: LAST / Resolution: 1.87→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3826 0 127 288 4241
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0224048
X-RAY DIFFRACTIONr_bond_other_d0.0010.022665
X-RAY DIFFRACTIONr_angle_refined_deg1.5571.9925497
X-RAY DIFFRACTIONr_angle_other_deg0.96436509
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7085516
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.99124.438169
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.83615671
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7091527
X-RAY DIFFRACTIONr_chiral_restr0.0950.2633
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024509
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02806
X-RAY DIFFRACTIONr_mcbond_it0.9031.52540
X-RAY DIFFRACTIONr_mcbond_other0.2711.51058
X-RAY DIFFRACTIONr_mcangle_it1.60124061
X-RAY DIFFRACTIONr_scbond_it2.95531508
X-RAY DIFFRACTIONr_scangle_it4.3274.51436
LS refinement shellResolution: 1.87→1.919 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 130 -
Rwork0.215 2605 -
obs--83.84 %
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)
10.18740.0614-0.01141.5921-1.01651.3173-0.0480.04630.011-0.27240.0288-0.02580.09390.07940.01920.0623-0.02350.00230.0873-0.01530.071720.4445.39224.046
20.18210.02790.02650.61540.13580.5619-0.02510.0151-0.0233-0.01570.04240.0270.07870.0385-0.01730.01730.00430.00230.1137-0.01040.098718.47740.06344.477
30.658-0.25030.16521.2681-0.13680.9059-0.05260.0403-0.0619-0.02190.0295-0.0009-0.02660.05690.02310.0063-0.0060.00890.07820.00120.050318.9443.80540.968
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 26
2X-RAY DIFFRACTION1B-2 - 78
3X-RAY DIFFRACTION2A27 - 171
4X-RAY DIFFRACTION2B79 - 170
5X-RAY DIFFRACTION3A172 - 252
6X-RAY DIFFRACTION3B171 - 252

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