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- PDB-1y8a: Structure of gene product AF1437 from Archaeoglobus fulgidus -

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Basic information

Entry
Database: PDB / ID: 1y8a
TitleStructure of gene product AF1437 from Archaeoglobus fulgidus
Componentshypothetical protein AF1437Hypothesis
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Archaeoglobus fulgidus / protein structure initiative / PSI / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


AF1437-like domain fold / AF1437-like domain superfamily / AF1437-like / [NiFe]-hydrogenase-3-type complex Eha, EhaR / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Helix non-globular / Special ...AF1437-like domain fold / AF1437-like domain superfamily / AF1437-like / [NiFe]-hydrogenase-3-type complex Eha, EhaR / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Helix non-globular / Special / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Uncharacterized protein
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.4 Å
AuthorsCuff, M.E. / Xu, X. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be published
Title: Structure of gene product AF1437 from Archaeoglobus fulgidus
Authors: Cuff, M.E. / Xu, X. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
History
DepositionDec 10, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

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Assembly

Deposited unit
A: hypothetical protein AF1437
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2642
Polymers37,2391
Non-polymers241
Water7,368409
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.900, 84.027, 44.175
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-731-

HOH

21A-900-

HOH

31A-907-

HOH

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Components

#1: Protein hypothetical protein AF1437 / Hypothesis


Mass: 37239.320 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Strain: DSM 4304 / Gene: AF1437 / Production host: Escherichia coli (E. coli) / References: UniProt: O28835
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 409 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 38.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: HEPES, MgCl2, PEG 3350, Glycerol , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11101
21101
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 19-BM10.97944
SYNCHROTRONAPS 19-BM20.97951
Detector
TypeIDDetectorDateDetails
CUSTOM-MADE1CCDOct 10, 2004SBC3
CUSTOM-MADE2CCDApr 18, 2004SBC3
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SAGITALLY FOCUSED Si(111)SINGLE WAVELENGTHMx-ray1
2SAGITALLY FOCUSED Si(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979441
20.979511
ReflectionResolution: 1.4→36.64 Å / Num. all: 53385 / Num. obs: 53385 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.4→1.45 Å / % possible all: 70.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHELXDphasing
MLPHAREphasing
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.4→36.64 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.454 / SU ML: 0.049 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.073 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2227 2710 5.1 %RANDOM
Rwork0.18278 ---
obs0.18479 50667 96.04 %-
all-53377 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.051 Å2
Baniso -1Baniso -2Baniso -3
1-0.71 Å20 Å20 Å2
2---0.17 Å20 Å2
3----0.54 Å2
Refinement stepCycle: LAST / Resolution: 1.4→36.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2459 0 1 409 2869
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222610
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1591.9693531
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0975334
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.68223.333120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.23715474
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6761523
X-RAY DIFFRACTIONr_chiral_restr0.0770.2386
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021994
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2020.21370
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.21857
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1090.2289
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1420.264
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1350.262
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6961.51660
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.12622604
X-RAY DIFFRACTIONr_scbond_it1.93831069
X-RAY DIFFRACTIONr_scangle_it3.0624.5927
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.401→1.437 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 118 -
Rwork0.234 2535 -
obs--65.39 %
Refinement TLS params.Method: refined / Origin x: 8.6936 Å / Origin y: 26.779 Å / Origin z: 12.2508 Å
111213212223313233
T-0.0283 Å20.0013 Å2-0.0028 Å2--0.0204 Å2-0.0113 Å2---0.0405 Å2
L0.554 °20.0314 °2-0.0883 °2-0.8171 °2-0.3122 °2--0.4053 °2
S0.0104 Å °0.0348 Å °-0.023 Å °-0.0199 Å °-0.0365 Å °-0.0092 Å °0.0028 Å °0.0089 Å °0.0261 Å °

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