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- PDB-2ph7: Crystal structure of AF2093 from Archaeoglobus fulgidus -

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Basic information

Entry
Database: PDB / ID: 2ph7
TitleCrystal structure of AF2093 from Archaeoglobus fulgidus
ComponentsUncharacterized protein AF_2093
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / AF2093 / Archaeoglobus fulgidus / SOUTHEAST COLLABORATORY FOR STRUCTURAL GENOMICS / SECSG / PSI / Protein Structure Initiative
Function / homology
Function and homology information


af_2093 domain like fold / af_2093 domain like / af2093 domain / Af2093, N-terminal / : / : / : / : / Domain of unknown function (DUF6834), C-terminal domain / Domain of unknown function (DUF6846) ...af_2093 domain like fold / af_2093 domain like / af2093 domain / Af2093, N-terminal / : / : / : / : / Domain of unknown function (DUF6834), C-terminal domain / Domain of unknown function (DUF6846) / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Uncharacterized protein AF_2093
Similarity search - Component
Biological speciesArchaeoglobus fulgidus DSM 4304 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsChang, J.C. / Yang, H. / Hwang, J. / Zhu, J. / Chen, L. / Fu, Z.-Q. / Xu, H. / Rose, J.P. / Wang, B.-C. / Southeast Collaboratory for Structural Genomics (SECSG)
CitationJournal: To be Published
Title: Crystal structure of AF2093 from Archaeoglobus fulgidus.
Authors: Chang, J.C. / Yang, H. / Hwang, J. / Zhu, J. / Chen, L. / Fu, Z.-Q. / Xu, H. / Rose, J.P. / Wang, B.-C.
History
DepositionApr 10, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.4Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Remark 999 SEQUENCE THE TARGET SEQUENCE INFORMATION IS AVAILABLE AT PEPCDB WITH ACCESSION CODE GL2-223-001.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein AF_2093
B: Uncharacterized protein AF_2093


Theoretical massNumber of molelcules
Total (without water)57,9452
Polymers57,9452
Non-polymers00
Water1,29772
1
A: Uncharacterized protein AF_2093


Theoretical massNumber of molelcules
Total (without water)28,9721
Polymers28,9721
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Uncharacterized protein AF_2093


Theoretical massNumber of molelcules
Total (without water)28,9721
Polymers28,9721
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)206.536, 206.536, 206.536
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number196
Space group name H-MF23

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Components

#1: Protein Uncharacterized protein AF_2093


Mass: 28972.256 Da / Num. of mol.: 2
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_2093 / Plasmid: pDest-527 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIPL / References: UniProt: O28187
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.17 Å3/Da / Density % sol: 61.16 %
Crystal growTemperature: 291 K / Method: modified microbatch / pH: 4.9
Details: USING 1.0 MICROLITER DROPS CONTAINING EQUAL VOLUMES OF PROTEIN CONCENTRATE (12 mg/mL) AND SOLUTION CONTAINING 20% PEG 4000, 0.05M SODIUM CHLORIDE, 0.05M LITHIUM SULFATE, 0.1M SODIUM ACETATE ...Details: USING 1.0 MICROLITER DROPS CONTAINING EQUAL VOLUMES OF PROTEIN CONCENTRATE (12 mg/mL) AND SOLUTION CONTAINING 20% PEG 4000, 0.05M SODIUM CHLORIDE, 0.05M LITHIUM SULFATE, 0.1M SODIUM ACETATE pH 4.9, Modified Microbatch, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9724 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 31, 2007 / Details: ROSENBAUM
RadiationMonochromator: SI CHANNEL 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9724 Å / Relative weight: 1
ReflectionResolution: 2.4→47.4 Å / Num. obs: 28734 / % possible obs: 99.9 % / Redundancy: 6.7 % / Rsym value: 0.066 / Net I/σ(I): 39.3
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 2.08 / Num. unique all: 2858 / Rsym value: 0.535 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SERGUIdata collection
HKL-2000data reduction
HKL-2000data scaling
SGXPROphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→47.4 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.915 / SU B: 8.002 / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.301 / ESU R Free: 0.242 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27143 1423 5 %RANDOM
Rwork0.23022 ---
obs0.23225 27283 99.9 %-
all-27283 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.574 Å2
Refinement stepCycle: LAST / Resolution: 2.4→47.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3583 0 0 72 3655
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223661
X-RAY DIFFRACTIONr_angle_refined_deg1.3411.9654921
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.2315435
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.58224180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.64415672
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5471521
X-RAY DIFFRACTIONr_chiral_restr0.2340.2527
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022755
X-RAY DIFFRACTIONr_nbd_refined0.2010.21511
X-RAY DIFFRACTIONr_nbtor_refined0.3060.22499
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2150
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1830.257
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1410.29
X-RAY DIFFRACTIONr_mcbond_it1.1721.52243
X-RAY DIFFRACTIONr_mcangle_it1.37223523
X-RAY DIFFRACTIONr_scbond_it1.8431588
X-RAY DIFFRACTIONr_scangle_it2.8814.51398
LS refinement shellResolution: 2.4→2.457 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.485 96 -
Rwork0.335 1984 -
obs--99.66 %

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