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- PDB-1htw: COMPLEX OF HI0065 WITH ADP AND MAGNESIUM -

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Basic information

Entry
Database: PDB / ID: 1htw
TitleCOMPLEX OF HI0065 WITH ADP AND MAGNESIUM
ComponentsHI0065
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / nucleotide-binding fold / Structure 2 Function Project / S2F
Function / homology
Function and homology information


tRNA threonylcarbamoyladenosine modification / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
tRNA threonylcarbamoyl adenosine modification protein TsaE / Threonylcarbamoyl adenosine biosynthesis protein TsaE / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / ADENOSINE-5'-DIPHOSPHATE / tRNA threonylcarbamoyladenosine biosynthesis protein TsaE
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.7 Å
AuthorsTeplyakov, A. / Gilliland, G.L. / Structure 2 Function Project (S2F)
CitationJournal: Proteins / Year: 2002
Title: Crystal structure of the YjeE protein from Haemophilus influenzae: a putative Atpase involved in cell wall synthesis
Authors: Teplyakov, A. / Obmolova, G. / Tordova, M. / Thanki, N. / Bonander, N. / Eisenstein, E. / Howard, A.J. / Gilliland, G.L.
History
DepositionJan 1, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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.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.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.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_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: HI0065
B: HI0065
C: HI0065
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,46614
Polymers53,9593
Non-polymers1,50711
Water7,332407
1
A: HI0065
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5446
Polymers17,9861
Non-polymers5585
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: HI0065
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4614
Polymers17,9861
Non-polymers4743
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: HI0065
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4614
Polymers17,9861
Non-polymers4743
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.350, 71.340, 95.700
Angle α, β, γ (deg.)90.00, 109.45, 90.00
Int Tables number5
Space group name H-MC121
Detailsprobably monomer

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein HI0065


Mass: 17986.488 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: HI0065 / Production host: Escherichia coli (E. coli) / References: UniProt: P44492

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Non-polymers , 5 types, 418 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 407 / 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: 2.31 Å3/Da / Density % sol: 46.67 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG4000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110 mg/mlprotein1drop
224 %(w/v)PEG40001reservoir
31 Msodium acetate1reservoir
410 mM1reservoirMgCl2
510 mMATP1reservoir
60.1 MHEPES1reservoirpH7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1.0642 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 18, 2000
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0642 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. all: 48750 / Num. obs: 48750 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8 % / Biso Wilson estimate: 40 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 15
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 8 % / Rmerge(I) obs: 0.12 / % possible all: 98
Reflection
*PLUS
Lowest resolution: 20 Å / % possible obs: 97 % / Num. measured all: 395260 / Rmerge(I) obs: 0.05
Reflection shell
*PLUS
Rmerge(I) obs: 0.12 / Mean I/σ(I) obs: 7

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Processing

Software
NameClassification
CNSrefinement
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1FL9

1fl9


Resolution: 1.7→15 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: 0.02
RfactorNum. reflectionSelection details
Rfree0.235 2500 random 5%
Rwork0.199 --
all0.199 48750 -
obs-48750 -
Refinement stepCycle: LAST / Resolution: 1.7→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3790 0 92 407 4289
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor all: 0.199 / Rfactor Rfree: 0.235 / Rfactor Rwork: 0.199
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.019
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_deg1.5

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