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- PDB-2oo2: Crystal structure of protein AF1782 from Archaeoglobus fulgidus, ... -

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Basic information

Entry
Database: PDB / ID: 2oo2
TitleCrystal structure of protein AF1782 from Archaeoglobus fulgidus, Pfam DUF357
ComponentsHypothetical protein AF_1782
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homologyDomain of unknown function DUF357 / AF1782-like superfamily / Protein of unknown function (DUF357) / AF1782-like / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Up-down Bundle / Mainly Alpha / DUF357 domain-containing protein
Function and homology information
Biological speciesArchaeoglobus fulgidus DSM 4304 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsBonanno, J.B. / Rutter, M. / Bain, K.T. / Adams, J. / Sridhar, V. / Smyth, L. / Freeman, J. / Atwell, S. / Sauder, J.M. / Burley, S.K. ...Bonanno, J.B. / Rutter, M. / Bain, K.T. / Adams, J. / Sridhar, V. / Smyth, L. / Freeman, J. / Atwell, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of the hypothetical AF_1782 protein from Archaeoglobus fulgidus
Authors: Bonanno, J.B. / Rutter, M. / Bain, K.T. / Adams, J. / Sridhar, V. / Smyth, L. / Freeman, J. / Atwell, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionJan 25, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 24, 2012Group: Structure summary
Revision 1.4Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.5Feb 3, 2021Group: Database references / Structure summary
Category: audit_author / citation_author / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details
Revision 1.6Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). AUTHORS STATE THAT THIS IS A PROBABLE DIMER.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical protein AF_1782


Theoretical massNumber of molelcules
Total (without water)10,3761
Polymers10,3761
Non-polymers00
Water41423
1
A: Hypothetical protein AF_1782

A: Hypothetical protein AF_1782


Theoretical massNumber of molelcules
Total (without water)20,7512
Polymers20,7512
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area1970 Å2
ΔGint-23 kcal/mol
Surface area8310 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)44.631, 46.452, 43.177
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Hypothetical protein AF_1782


Mass: 10375.664 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus DSM 4304 (archaea)
Species: Archaeoglobus fulgidus / Strain: VC-16, DSM 4304, JCM 9628, NBRC 100126 / Gene: AF_1782 / Plasmid: modified pET26 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O28492
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.16 Å3/Da / Density % sol: 42.97 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 7.5
Details: 100mM Tris-HCl pH 7.5, 3.2M 1,6-hexanediol, 200mM Magnesium chloride, VAPOR DIFFUSION, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.97958 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 20, 2007
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97958 Å / Relative weight: 1
ReflectionResolution: 1.795→43.193 Å / Num. all: 8822 / Num. obs: 8690 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.9 % / Biso Wilson estimate: 28 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 20.6
Reflection shellResolution: 1.795→1.89 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.549 / Mean I/σ(I) obs: 2.4 / Num. measured all: 7358 / Num. unique all: 1147 / Rsym value: 0.549 / % possible all: 91.8

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.91 / SU B: 4.256 / SU ML: 0.132 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.152 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.289 415 4.8 %RANDOM
Rwork0.24 ---
obs0.242 8682 98.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 39.037 Å2
Baniso -1Baniso -2Baniso -3
1--1.8 Å20 Å20 Å2
2---3.21 Å20 Å2
3---5.01 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms645 0 0 23 668
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.022658
X-RAY DIFFRACTIONr_angle_refined_deg1.9541.947885
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.689575
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.74323.51437
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.27615125
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.836157
X-RAY DIFFRACTIONr_chiral_restr0.1320.292
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02498
X-RAY DIFFRACTIONr_nbd_refined0.2110.2268
X-RAY DIFFRACTIONr_nbtor_refined0.2950.2446
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.233
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2110.227
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2820.26
X-RAY DIFFRACTIONr_mcbond_it1.6211.5392
X-RAY DIFFRACTIONr_mcangle_it2.2662598
X-RAY DIFFRACTIONr_scbond_it3.883326
X-RAY DIFFRACTIONr_scangle_it5.8754.5287
LS refinement shellResolution: 1.8→1.84 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 35 -
Rwork0.343 512 -
obs-547 87.52 %

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