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- PDB-1mw5: Structure of HI1480 from Haemophilus influenzae -

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Basic information

Entry
Database: PDB / ID: 1mw5
TitleStructure of HI1480 from Haemophilus influenzae
ComponentsHYPOTHETICAL PROTEIN HI1480
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / hypothetical protein / Structure 2 Function Project / S2F
Function / homologyZinc Finger, Delta Prime; domain 3 - #30 / Hypothetical protein HI1480 / Hypothetical protein HI1480 / Zinc Finger, Delta Prime; domain 3 / Up-down Bundle / Mainly Alpha / Uncharacterized protein HI_1480
Function and homology information
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsLim, K. / Sarikaya, E. / Howard, A. / Galkin, A. / Herzberg, O. / Structure 2 Function Project (S2F)
CitationJournal: PROTEINS: STRUCT.,FUNCT.,GENET. / Year: 2004
Title: Novel structure and nucleotide binding properties of HI1480 from Haemophilus influenzae: a protein with no known sequence homologues
Authors: Lim, K. / Sarikaya, E. / Galkin, A. / Krajewski, W. / Pullalarevu, S. / Shin, J.H. / Kelman, Z. / Howard, A. / Herzberg, O.
History
DepositionSep 27, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Oct 30, 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

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Assembly

Deposited unit
A: HYPOTHETICAL PROTEIN HI1480
B: HYPOTHETICAL PROTEIN HI1480


Theoretical massNumber of molelcules
Total (without water)42,4352
Polymers42,4352
Non-polymers00
Water3,765209
1
A: HYPOTHETICAL PROTEIN HI1480
B: HYPOTHETICAL PROTEIN HI1480

A: HYPOTHETICAL PROTEIN HI1480
B: HYPOTHETICAL PROTEIN HI1480


Theoretical massNumber of molelcules
Total (without water)84,8714
Polymers84,8714
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655-x+1,-y,z1
Unit cell
Length a, b, c (Å)79.289, 79.289, 143.842
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64
DetailsDimer of dimers. The tetramer is generated from the dimer of the asymmetric unit by a crystallographic symmetry: 1-X,-Y,Z

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Components

#1: Protein HYPOTHETICAL PROTEIN HI1480


Mass: 21217.662 Da / Num. of mol.: 2 / Mutation: L8M, F151M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: HI1480 / Plasmid: pET100 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P44209
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / 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: 3.07 Å3/Da / Density % sol: 59.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 8% PEG 8000, 0.2M MgCl2, 0.1M Tris-HCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
17 %PEG80001reservoir
20.1 MTris-HCl1reservoirpH7.0
30.2 M1reservoirMgCl2
420 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 5, 2002
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 29494 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.06 / Net I/σ(I): 9
Reflection shellResolution: 2.1→2.2 Å / Rmerge(I) obs: 0.312 / Mean I/σ(I) obs: 7.2 / Num. unique all: 3690 / % possible all: 100
Reflection
*PLUS
Num. obs: 58739 / Num. measured all: 341570 / Rmerge(I) obs: 0.055
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.255

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXDphasing
MLPHAREphasing
DMmodel building
ARP/wARPmodel building
CNSrefinement
DMphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→20 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.243 2678 random
Rwork0.196 --
all-28556 -
obs-27084 -
Displacement parametersBiso mean: 42 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2648 0 0 209 2857
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.016
X-RAY DIFFRACTIONc_angle_deg1.6
LS refinement shellResolution: 2.1→2.2 Å / Rfactor Rfree: 0.28 / Rfactor Rwork: 0.23
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor Rfree: 0.244 / Rfactor Rwork: 0.197
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_bond_d / Dev ideal: 0.015
LS refinement shell
*PLUS
Rfactor Rfree: 0.278 / Rfactor Rwork: 0.208

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