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- PDB-1y7p: 1.9 A Crystal Structure of a Protein of Unknown Function AF1403 f... -

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Basic information

Entry
Database: PDB / ID: 1y7p
Title1.9 A Crystal Structure of a Protein of Unknown Function AF1403 from Archaeoglobus fulgidus, Probable Metabolic Regulator
ComponentsHypothetical protein AF1403
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Protein structure initiative / PSI / Archaeoglobus fulgidus / alpha-beta-alpha sandwich / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


Hypothetical protein af1403; domain 2 / Uncharacterised conserved protein UCP006363, ACT-type / Domain of unknown function DUF5612 / Domain of unknown function (DUF5612) / ACT domain / ACT domain / ACT domain profile. / ACT domain / CheY-like superfamily / Alpha-Beta Plaits ...Hypothetical protein af1403; domain 2 / Uncharacterised conserved protein UCP006363, ACT-type / Domain of unknown function DUF5612 / Domain of unknown function (DUF5612) / ACT domain / ACT domain / ACT domain profile. / ACT domain / CheY-like superfamily / Alpha-Beta Plaits / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
beta-D-ribopyranose / Uncharacterized protein AF_1403
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsZhang, R. / Skarina, T. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: 1.9A crystal structure of a hypothetical protein AF1403 from Archaeoglobus fulgidus
Authors: Zhang, R. / Skarina, T. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
History
DepositionDec 9, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypothetical protein AF1403
B: Hypothetical protein AF1403
C: Hypothetical protein AF1403
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,0109
Polymers73,3633
Non-polymers6476
Water4,216234
1
A: Hypothetical protein AF1403
C: Hypothetical protein AF1403
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3406
Polymers48,9092
Non-polymers4314
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6510 Å2
ΔGint-88 kcal/mol
Surface area17350 Å2
MethodPISA
2
B: Hypothetical protein AF1403
hetero molecules

B: Hypothetical protein AF1403
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3406
Polymers48,9092
Non-polymers4314
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
3
B: Hypothetical protein AF1403
hetero molecules

B: Hypothetical protein AF1403
hetero molecules

A: Hypothetical protein AF1403
C: Hypothetical protein AF1403
hetero molecules

A: Hypothetical protein AF1403
C: Hypothetical protein AF1403
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,02018
Polymers146,7266
Non-polymers1,29312
Water1086
TypeNameSymmetry operationNumber
crystal symmetry operation3_555-y+1/2,x+1/2,z+1/41
crystal symmetry operation5_555-x+1/2,y+1/2,-z+1/41
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area27430 Å2
ΔGint-343 kcal/mol
Surface area43660 Å2
MethodPISA
4
C: Hypothetical protein AF1403
hetero molecules

B: Hypothetical protein AF1403
hetero molecules

A: Hypothetical protein AF1403
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,0109
Polymers73,3633
Non-polymers6476
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-y+1/2,x+1/2,z+1/41
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area4300 Å2
ΔGint-137 kcal/mol
Surface area31240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.709, 95.709, 167.551
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsThis protein existed as dimer. The deposited coords. of MolA and MolD form the biological dimer.

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Components

#1: Protein Hypothetical protein AF1403


Mass: 24454.412 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Strain: VC-16-DSM4304-ATCC49558 / Gene: AF1403 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: O28869
#2: Sugar ChemComp-RIP / beta-D-ribopyranose / beta-D-ribose / D-ribose / ribose / RIBOSE(PYRANOSE FORM)


Type: D-saccharide, beta linking / Mass: 150.130 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C5H10O5
IdentifierTypeProgram
DRibpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-ribopyranoseCOMMON NAMEGMML 1.0
b-D-RibpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
RibSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 234 / 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: 1.958 Å3/Da / Density % sol: 35 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.2 M K/Na Tartr., 20% PEG3350, 0.05M Tris buffer, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9798 Å
DetectorType: SBC-2 / Detector: CCD / Date: Mar 7, 2004 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. all: 117308 / Num. obs: 102527 / % possible obs: 87.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.9 % / Biso Wilson estimate: 15.3 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 22.6
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.495 / Mean I/σ(I) obs: 1.534 / % possible all: 85.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
SBC-Collectdata collection
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→36.34 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 392525.79 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.255 5082 5 %RANDOM
Rwork0.211 ---
obs0.211 102527 87.4 %-
all-117308 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 65.6118 Å2 / ksol: 0.374876 e/Å3
Displacement parametersBiso mean: 39 Å2
Baniso -1Baniso -2Baniso -3
1-4.75 Å20 Å20 Å2
2--4.75 Å20 Å2
3----9.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 1.9→36.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4898 0 33 234 5165
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.7
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.333 754 5.3 %
Rwork0.311 13601 -
obs--73.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMRIP.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4RIP.PAR

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