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- PDB-1izm: Structure of ygfB from Haemophilus influenzae (HI0817), a Conserv... -

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Basic information

Entry
Database: PDB / ID: 1izm
TitleStructure of ygfB from Haemophilus influenzae (HI0817), a Conserved Hypothetical Protein
ComponentsHYPOTHETICAL PROTEIN HI0817
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / hypothetical protein / HI0817 / ygfB / Structure 2 Function Project / S2F
Function / homologyYgfB uncharacterised protein family PF03695 / YgfB-like / YgfB-like superfamily / Uncharacterised protein family (UPF0149) / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha / cytosol / UPF0149 protein HI_0817
Function and homology information
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.95 Å
AuthorsGalkin, A. / Sarikaya, E. / Lehmann, C. / Howard, A. / Herzberg, O. / Structure 2 Function Project (S2F)
CitationJournal: Proteins / Year: 2004
Title: X-ray structure of HI0817 from Haemophilus influenzae: protein of unknown function with a novel fold.
Authors: Galkin, A. / Sarikaya, E. / Lehmann, C. / Howard, A. / Herzberg, O.
History
DepositionOct 9, 2002Deposition site: PDBJ / Processing site: RCSB
Revision 1.0Dec 2, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: HYPOTHETICAL PROTEIN HI0817


Theoretical massNumber of molelcules
Total (without water)20,6041
Polymers20,6041
Non-polymers00
Water3,621201
1
A: HYPOTHETICAL PROTEIN HI0817

A: HYPOTHETICAL PROTEIN HI0817


Theoretical massNumber of molelcules
Total (without water)41,2082
Polymers41,2082
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_466y-1,x+1,-z+11
Unit cell
Length a, b, c (Å)42.3, 42.3, 198.5
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsDimer.The asymmetric unit contains one monomer. The dimer is generated from the monomer by a crystallographic symmetry: Y-1, X+1,-Z+1

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Components

#1: Protein HYPOTHETICAL PROTEIN HI0817


Mass: 20604.152 Da / Num. of mol.: 1 / Mutation: L8M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: HI0817 / Plasmid: pET100 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P44882
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / 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: 2.15 Å3/Da / Density % sol: 42.92 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 1.4 M ammonimum sulfate, 0.05 M potassium phosphate, 3% iso-propanol, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
150 mMTris-HCl1droppH7.0
2150 mM1dropNaCl
31.4 Mammonium sulfate1reservoir
40.05 Mpotassium phosphate1reservoirpH4.8
54 %isopropanol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.97946, 0.97961, 0.96863
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 6, 2001
RadiationMonochromator: Si(111) double crystal system / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979461
20.979611
30.968631
ReflectionResolution: 1.95→20 Å / Num. all: 14167 / Num. obs: 14167 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.05 / Net I/σ(I): 21.1
Reflection shellResolution: 1.95→2.02 Å / Rmerge(I) obs: 0.097 / % possible all: 91.9
Reflection
*PLUS
Num. obs: 24638 / % possible obs: 98 % / Num. measured all: 298675 / Rmerge(I) obs: 0.05
Reflection shell
*PLUS
% possible obs: 92 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEmodel building
CNS1refinement
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.95→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.255 951 -random
Rwork0.194 ---
all-14054 --
obs-13482 95.9 %-
Displacement parametersBiso mean: 38 Å2
Refinement stepCycle: LAST / Resolution: 1.95→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1336 0 0 201 1537
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.02
X-RAY DIFFRACTIONc_angle_d1.8
LS refinement shellResolution: 1.95→2.02 Å
RfactorNum. reflection
Rfree0.305 84
Rwork0.215 -
obs-1193
Refine LS restraints
*PLUS
Type: c_bond_d / Dev ideal: 0.02

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