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- PDB-3k67: Crystal structure of protein af1124 from archaeoglobus fulgidus -

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Basic information

Entry
Database: PDB / ID: 3k67
TitleCrystal structure of protein af1124 from archaeoglobus fulgidus
Componentsputative dehydratase AF1124
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / HYPOTHETICAL PROTEIN AF1124 / PSI / PROTEIN STRUCTURE INITIATIVE / MIDWEST CENTER FOR STRUCTURAL GENOMICS / MCSG
Function / homology
Function and homology information


fatty acid synthase complex / (3R)-hydroxyacyl-[acyl-carrier-protein] dehydratase activity / fatty acid synthase activity / fatty acid biosynthetic process
Similarity search - Function
: / Fatty acid synthase / MaoC-like dehydratase domain / MaoC like domain / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / MaoC-like domain-containing protein
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsChang, C. / Skarina, T. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of Protein Af1124 from Archaeoglobus Fulgidus
Authors: Chang, C. / Skarina, T. / Savchenko, A. / Edwards, A. / Joachimiak, A.
History
DepositionOct 8, 2009Deposition site: RCSB / Processing site: RCSB
SupersessionOct 20, 2009ID: 2B3N
Revision 1.0Oct 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 dehydratase AF1124
B: putative dehydratase AF1124
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3583
Polymers35,2632
Non-polymers951
Water6,557364
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6000 Å2
ΔGint-58 kcal/mol
Surface area13050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.973, 55.320, 69.121
Angle α, β, γ (deg.)90.00, 93.36, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein putative dehydratase AF1124


Mass: 17631.512 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: AF_1124 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O29141
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 364 / 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: 2.4 Å3/Da / Density % sol: 49.1 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: AMMONIUM PHOSPHATE, TRIS HCL, PH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97942 / Wavelength: 0.97942 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 21, 2005
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 1.25→50 Å / Num. all: 93720 / Num. obs: 90451 / % possible obs: 96.5 % / Observed criterion σ(I): -3 / Redundancy: 9 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 57.1
Reflection shellResolution: 1.25→1.29 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.296 / Mean I/σ(I) obs: 6.6 / % possible all: 92.3

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Processing

Software
NameVersionClassification
AMoREphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 2B3M (SEL-MET DERIVATIVE)

2b3m


Resolution: 1.25→50 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.97 / SU B: 0.956 / SU ML: 0.02 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.043 / ESU R Free: 0.04 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16559 4536 5 %RANDOM
Rwork0.14569 ---
all0.14671 90428 --
obs0.14671 90428 96.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.145 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å2-0.03 Å2
2--0.4 Å20 Å2
3----0.39 Å2
Refinement stepCycle: LAST / Resolution: 1.25→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2678 0 5 364 3047
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222765
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5921.9853781
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0675392
X-RAY DIFFRACTIONr_dihedral_angle_2_deg22.1523.982113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.96415535
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.291517
X-RAY DIFFRACTIONr_chiral_restr0.1130.2426
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212089
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5861.51706
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.51722811
X-RAY DIFFRACTIONr_scbond_it3.59931059
X-RAY DIFFRACTIONr_scangle_it5.5114.5942
X-RAY DIFFRACTIONr_rigid_bond_restr1.57832765
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.249→1.282 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 332 -
Rwork0.215 6011 -
obs--91.58 %
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)
10.488-0.283-0.09090.34660.58781.63740.0074-0.09150.1128-0.04880.0887-0.0886-0.16660.1495-0.09610.0543-0.0270.01730.0471-0.04550.060110.417213.506320.4286
20.40490.0630.02480.3857-0.05870.53330.00990.0104-0.0499-0.03110.0388-0.0418-0.00110.0412-0.04870.0133-0.00310.00250.0122-0.00880.01967.3594-3.439.9738
30.30310.32730.28860.9105-0.0390.66020.0216-0.1001-0.00250.0697-0.00140.0252-0.0182-0.1437-0.02020.0301-0.00290.00720.05980.00920.0064-6.3192-1.151529.0095
40.36710.06930.34171.33540.33780.6673-0.029-0.13910.05270.1082-0.00050.0777-0.0853-0.12270.02950.05720.02260.02110.0804-0.02540.0248-8.89512.039627.6797
50.61380.0983-0.02910.39640.08770.24260.0191-0.0114-0.0446-0.0124-0.0290.0498-0.0249-0.04240.00990.01230.0018-0.00350.02570.01230.0242-13.6660.472111.8452
61.09-0.1480.08210.2664-0.27671.1251-0.01910.09580.11790.02570.0106-0.0343-0.09460.07910.00850.0481-0.012800.02590.00170.02054.633515.08558.8923
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 32
2X-RAY DIFFRACTION2A33 - 49
3X-RAY DIFFRACTION2A83 - 159
4X-RAY DIFFRACTION3A50 - 82
5X-RAY DIFFRACTION4B7 - 32
6X-RAY DIFFRACTION5B33 - 49
7X-RAY DIFFRACTION5B83 - 159
8X-RAY DIFFRACTION6B50 - 82

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