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- PDB-1ve0: Crystal structure of uncharacterized protein ST2072 from Sulfolob... -

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Basic information

Entry
Database: PDB / ID: 1ve0
TitleCrystal structure of uncharacterized protein ST2072 from Sulfolobus tokodaii
Componentshypothetical protein (ST2072)
KeywordsMETAL BINDING PROTEIN / Structural genomics / Zinc binding protein
Function / homologyUncharacterized protein family UPF0047 signature. / YjbQ-like / Uncharacterised protein family UPF0047, YjbQ / YjbQ-like superfamily / UPF0047 protein YjbQ-like / Jelly Rolls / Sandwich / Mainly Beta / YjbQ family protein
Function and homology information
Biological speciesSulfolobus tokodaii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsTanabe, E. / Horiike, Y. / Tsumoto, K. / Yasutake, Y. / Yao, M. / Tanaka, I. / Kumagai, I.
CitationJournal: To be Published
Title: Crystal structure of the uncharacterized protein ST2072 from Sulfolobus tokodaii
Authors: Tanabe, E. / Horiike, Y. / Tsumoto, K. / Yasutake, Y. / Yao, M. / Tanaka, I. / Kumagai, I.
History
DepositionMar 26, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_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_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: hypothetical protein (ST2072)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2383
Polymers15,0771
Non-polymers1612
Water81145
1
A: hypothetical protein (ST2072)
hetero molecules

A: hypothetical protein (ST2072)
hetero molecules

A: hypothetical protein (ST2072)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7159
Polymers45,2313
Non-polymers4846
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_564-z+1/2,-x+1,y-1/21
crystal symmetry operation10_655-y+1,z+1/2,-x+1/21
Buried area8910 Å2
ΔGint-216 kcal/mol
Surface area13850 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)71.720, 71.720, 71.720
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
DetailsThe biological assembly must be a trimer generated from the monomer in the asymmetric unit by the operations: (1/2-z, 1-x, -1/2+y) and (1-y, 1/2+z ,1/2-x).

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Components

#1: Protein hypothetical protein (ST2072)


Mass: 15076.947 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus tokodaii (archaea) / Gene: ST2072 / Plasmid: pET20b / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q96YV5
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.04 Å3/Da / Density % sol: 39.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: 0.1M Tris-HCl pH8.2, 20% PEG4000, 0.2M LiSO4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 0.9789, 0.9794, 0.9000
DetectorType: ADSC / Detector: CCD / Date: Nov 23, 2003
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97891
20.97941
30.91
ReflectionResolution: 2→50 Å / Num. all: 8590 / Num. obs: 8590 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 21.5 % / Biso Wilson estimate: 38.23 Å2 / Rsym value: 0.065 / Net I/σ(I): 10.6
Reflection shellResolution: 2→2.07 Å / Redundancy: 21.8 % / Num. unique all: 853 / Rsym value: 0.389 / % possible all: 100

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
RefinementMethod to determine structure: MAD / Resolution: 2→10 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.222 832 -RANDOM
Rwork0.181 ---
all-8458 --
obs-8458 100 %-
Displacement parametersBiso mean: 26.18 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.07 Å
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1049 0 6 45 1100
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007126
X-RAY DIFFRACTIONc_angle_deg1.4169
X-RAY DIFFRACTIONc_dihedral_angle_d25.16596
X-RAY DIFFRACTIONc_improper_angle_d0.82954
X-RAY DIFFRACTIONc_mcangle_it2.362
X-RAY DIFFRACTIONc_mcbond_it1.386
X-RAY DIFFRACTIONc_scangle_it3.409
X-RAY DIFFRACTIONc_scbond_it2.063
LS refinement shellResolution: 2→2.07 Å
RfactorNum. reflection% reflection
Rfree0.213 82 -
Rwork0.163 --
obs-822 100 %

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