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- PDB-3ov8: Crystal structure of AF1382 from Archaeoglobus fulgidus, High res... -

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Basic information

Entry
Database: PDB / ID: 3ov8
TitleCrystal structure of AF1382 from Archaeoglobus fulgidus, High resolution
ComponentsProtein AF_1382
KeywordsUNKNOWN FUNCTION / AF1382 / PSI / STRUCTURAL GENOMICS / SOUTHEAST COLLABORATORY FOR STRUCTURAL GENOMICS / SECSG / putative DNS binding
Function / homologyWinged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha / ACETATE ION / Uncharacterized protein AF_1382
Function and homology information
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.8501 Å
AuthorsZhu, J.-Y. / Zhao, M. / Fu, Z.-Q. / Yang, H. / Chang, J. / Hao, X. / Chen, L. / Rose, J.P. / Wang, B.C. / Southeast Collaboratory for Structural Genomics (SECSG)
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Structure of the Archaeoglobus fulgidus orphan ORF AF1382 determined by sulfur SAD from a moderately diffracting crystal.
Authors: Zhu, J.Y. / Fu, Z.Q. / Chen, L. / Xu, H. / Chrzas, J. / Rose, J. / Wang, B.C.
History
DepositionSep 16, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2012Group: Atomic model / Data collection
Revision 1.2Jul 4, 2012Group: Database references
Revision 1.3Sep 19, 2012Group: Database references
Revision 1.4Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.5Sep 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: Protein AF_1382
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2894
Polymers11,1591
Non-polymers1303
Water1,36976
1
A: Protein AF_1382
hetero molecules

A: Protein AF_1382
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5788
Polymers22,3182
Non-polymers2606
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area3290 Å2
ΔGint-48 kcal/mol
Surface area9830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.033, 53.033, 40.968
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number77
Space group name H-MP42
Components on special symmetry positions
IDModelComponents
11A-105-

HOH

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Components

#1: Protein Protein AF_1382


Mass: 11159.016 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: AF1382, AF_1382 / Plasmid: pDEST-527 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RPX / References: UniProt: O28889
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.7 Å3/Da / Density % sol: 54.4 % / Description: STARTING MODEL FROM SULFUR SAD
Crystal growTemperature: 291 K / Method: modified macrobatch / pH: 4.6
Details: Microbatch using 1.0 microliter drops containing equal volumes of protein concentrate (2.8 mg/ml) and solution containg 0.2 M ammonium sulfate, 0.1 M sodium acetate, 30% w/v polyethylene ...Details: Microbatch using 1.0 microliter drops containing equal volumes of protein concentrate (2.8 mg/ml) and solution containg 0.2 M ammonium sulfate, 0.1 M sodium acetate, 30% w/v polyethylene glycol monomethyl ether, temperature 291k, pH 4.6, modified macrobatch

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9724 / Wavelength: 0.974 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 1, 2007 / Details: ROSENBAUM
RadiationMonochromator: SI CHANNEL 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97241
20.9741
ReflectionResolution: 1.85→50 Å / Num. all: 9876 / Num. obs: 9859 / % possible obs: 99.9 % / Redundancy: 13.3 % / Rsym value: 0.051 / Net I/σ(I): 60.66
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 12.5 % / Mean I/σ(I) obs: 12.96 / Rsym value: 0.233 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.6.4_486refinement
CNS1.3refinement
HKL-2000data reduction
HKL-2000data scaling
CNS1.3phasing
SERGUIdata collection
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 3O3K

3o3k


Resolution: 1.8501→37.5 Å / SU ML: 0.21 / Isotropic thermal model: RESTRAINED / σ(F): 0 / Phase error: 20.06 / Stereochemistry target values: ML / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflection
Rfree0.2145 493 5.05 %
Rwork0.1786 --
obs0.1804 9761 98.97 %
all-9876 -
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.004 Å2 / ksol: 0.344 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.5977 Å2-0 Å20 Å2
2---0.5977 Å2-0 Å2
3---1.1953 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.8501→37.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms748 0 6 76 830
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008774
X-RAY DIFFRACTIONf_angle_d0.9981038
X-RAY DIFFRACTIONf_dihedral_angle_d14.608307
X-RAY DIFFRACTIONf_chiral_restr0.067118
X-RAY DIFFRACTIONf_plane_restr0.003128
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8501-2.03630.25011170.20712270X-RAY DIFFRACTION97
2.0363-2.33090.24171270.17542290X-RAY DIFFRACTION99
2.3309-2.93650.23951230.1762339X-RAY DIFFRACTION100
2.9365-37.50770.18811260.17552369X-RAY DIFFRACTION100
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)
11.6152-1.4809-1.25431.6931.50281.4278-0.5176-0.0556-0.6056-0.2629-0.0680.80.2059-0.06160.55040.48530.03-0.00570.1146-0.04110.2874-6.146526.075512.7178
20.45110.10390.01940.0483-0.08591.02780.03890.0309-0.13370.0285-0.02710.03480.0416-0.2159-0.01220.1566-0.01320.0150.044-0.01790.117-0.83759.321617.3476
31.60790.7326-0.3723.66591.23961.5714-0.01170.209-0.0951-0.304-0.0987-0.4644-0.45140.07590.10080.2076-0.02060.00580.15050.01840.1688.071813.46089.9226
41.231-0.3873-0.32242.598-0.5020.8437-0.2124-0.0086-0.08840.69340.14440.07430.14790.06140.08780.2264-0.0413-0.01740.0563-0.0130.10622.929415.084121.3403
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 4:12)
2X-RAY DIFFRACTION2(chain A and resid 13:41)
3X-RAY DIFFRACTION3(chain A and resid 42:58)
4X-RAY DIFFRACTION4(chain A and resid 59:94)
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION6act.paract.top

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