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- PDB-1jog: Structure of HI0074 from Heamophilus Influenzae reveals the fold ... -

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Basic information

Entry
Database: PDB / ID: 1jog
TitleStructure of HI0074 from Heamophilus Influenzae reveals the fold of a substrate binding domain of a nucleotidyltransferase
ComponentsHYPOTHETICAL PROTEIN HI0074
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / HI0074 / hypothetical protein / Structure 2 Function Project / S2F
Function / homology
Function and homology information


endonuclease activity / Hydrolases; Acting on ester bonds / nucleotide binding
Similarity search - Function
Probable ribonuclease HepT / Nucleotidyltransferase substrate binding protein like / Nucleotidyltransferases domain 2 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Probable ribonuclease HepT
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsLehmann, C. / Lim, K. / Herzberg, O. / Structure 2 Function Project (S2F)
CitationJournal: Proteins / Year: 2003
Title: The HI0073/HI0074 protein pair from Haemophilus influenzae is a member of a new nucleotidyltransferase family: Structure, sequence analyses, and solution studies
Authors: Lehmann, C. / Lim, K. / Chalamasetty, V.R. / Krajewski, W. / Melamud, E. / Galkin, A. / Howard, A. / Kelman, Z. / Reddy, P.T. / Murzin, A.G. / Herzberg, O.
History
DepositionJul 29, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HYPOTHETICAL PROTEIN HI0074
B: HYPOTHETICAL PROTEIN HI0074
C: HYPOTHETICAL PROTEIN HI0074
D: HYPOTHETICAL PROTEIN HI0074


Theoretical massNumber of molelcules
Total (without water)70,0754
Polymers70,0754
Non-polymers00
Water2,522140
1
A: HYPOTHETICAL PROTEIN HI0074
B: HYPOTHETICAL PROTEIN HI0074


Theoretical massNumber of molelcules
Total (without water)35,0372
Polymers35,0372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2110 Å2
ΔGint-17 kcal/mol
Surface area13690 Å2
MethodPISA
2
C: HYPOTHETICAL PROTEIN HI0074
D: HYPOTHETICAL PROTEIN HI0074


Theoretical massNumber of molelcules
Total (without water)35,0372
Polymers35,0372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2080 Å2
ΔGint-17 kcal/mol
Surface area13680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.3, 87.1, 165.6
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121
DetailsProbably a dimer. The asymmetric unit contains two dimers.

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Components

#1: Protein
HYPOTHETICAL PROTEIN HI0074


Mass: 17518.633 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: HI0074 / Plasmid: pRE1 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P43934
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 1.97 Å3/Da / Density % sol: 37.59 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 30% PEG 4000, 0.1 M Tris, 0.2 M Na acetate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal grow
*PLUS
pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
14.7 mg/mlprotein1drop
2100 mM1dropNaCl
320 mMTris-HCl1droppH7.5
41 mMdithiothreitol1drop
51 mMEDTA1drop
630 %PEG40001reservoir
70.1 MTris-HCl1reservoirpH8.0
80.2 Msodium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.9791, 0.9793, 1.00
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 30, 2001 / Details: mirror
RadiationMonochromator: Si (111) double crystal system / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97911
20.97931
311
ReflectionResolution: 2.4→30 Å / Num. all: 22467 / Num. obs: 22467 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 6.8
Reflection shellResolution: 2.4→2.51 Å / Rmerge(I) obs: 0.314 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 30 Å

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXDphasing
MLPHAREphasing
DMmodel building
CNSrefinement
DMphasing
RefinementMethod to determine structure: MAD / Resolution: 2.4→20 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.282 1018 random
Rwork0.211 --
all-21646 -
obs-20694 -
Displacement parametersBiso mean: 57 Å2
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4423 0 0 140 4563
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.02
X-RAY DIFFRACTIONc_angle_deg2.1
LS refinement shellResolution: 2.4→2.49 Å / Rfactor Rfree: 0.334 / Rfactor Rwork: 0.258
Refinement
*PLUS
Lowest resolution: 20 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 2.1

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