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- PDB-1in0: YAJQ PROTEIN (HI1034) -

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Basic information

Entry
Database: PDB / ID: 1in0
TitleYAJQ PROTEIN (HI1034)
ComponentsYAJQ PROTEIN
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / alpha and beta sandwich / Structure 2 Function Project / S2F
Function / homology
Function and homology information


nucleotide binding / cytosol
Similarity search - Function
YajQ-like, domain 2 / Protein of unknown function DUF520 / UPF0234, N-terminal / YajQ-like superfamily / Protein of unknown function (DUF520) / Alpha-Beta Plaits - #860 / UPF0234-like, C-terminal / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / METHYL MERCURY ION / UPF0234 protein HI_1034
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.14 Å
AuthorsTeplyakov, A. / Gilliland, G.L. / Structure 2 Function Project (S2F)
CitationJournal: J.STRUCT.FUNCT.GENOM. / Year: 2003
Title: Crystal structure of the YajQ protein from Haemophilus influenzae reveals a tandem of RNP-like domains
Authors: Teplyakov, A. / Obmolova, G. / Bir, N. / Reddy, P. / Howard, A.J. / Gilliland, G.L.
History
DepositionMay 11, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: 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_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_asym_id / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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.ptnr2_symmetry / _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

Downloads & links

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Assembly

Deposited unit
A: YAJQ PROTEIN
B: YAJQ PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0208
Polymers37,1562
Non-polymers8636
Water6,395355
1
A: YAJQ PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0174
Polymers18,5781
Non-polymers4393
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: YAJQ PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0024
Polymers18,5781
Non-polymers4243
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.800, 62.800, 194.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322

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Components

#1: Protein YAJQ PROTEIN / HI1034


Mass: 18578.146 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: yajQ / Production host: Escherichia coli (E. coli) / References: UniProt: P44096
#2: Chemical ChemComp-HG / MERCURY (II) ION / Mercury (element)


Mass: 200.590 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Hg
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-MMC / METHYL MERCURY ION / Methylmercury


Mass: 215.625 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH3Hg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 355 / 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: 2.58 Å3/Da / Density % sol: 52.33 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Na Formate, MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1reservoir
24.5-5.0 Msodium formate1reservoir
33 %dioxane1reservoir
450 mMMES1reservoirpH6.0
515 mg/mlprotein1drop
650 mMTris-HCl1droppH7.5
71 mMEDTA1drop
81 mMdithiothreitol1drop
90.1 mMPMSF1drop
10100 mM1dropNaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 0.9686 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 9, 2001
RadiationMonochromator: graphite / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.14→20 Å / Num. all: 22433 / Num. obs: 22433 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.6 % / Biso Wilson estimate: 28 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 36.5
Reflection shellResolution: 2.14→2.19 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.118 / Mean I/σ(I) obs: 11.7 / Num. unique all: 1462 / % possible all: 100
Reflection
*PLUS
Highest resolution: 2.1 Å / Num. obs: 22374 / Num. measured all: 215822

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
REFMACrefinement
RefinementMethod to determine structure: MAD / Resolution: 2.14→8 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rwork0.193 --
all-21903 -
obs-21903 100 %
Refinement stepCycle: LAST / Resolution: 2.14→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2592 0 7 355 2954
Refine LS restraintsType: p_bond_d / Dev ideal: 0.013
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor Rfree: 0.268
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2.6

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