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- PDB-1mww: THE STRUCTURE OF THE HYPOTHETICAL PROTEIN HI1388.1 FROM HAEMOPHIL... -

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Basic information

Entry
Database: PDB / ID: 1mww
TitleTHE STRUCTURE OF THE HYPOTHETICAL PROTEIN HI1388.1 FROM HAEMOPHILUS INFLUENZAE REVEALS A TAUTOMERASE/MIF FOLD
ComponentsHYPOTHETICAL PROTEIN HI1388.1
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / I1388.1 / HYPOTHETICAL PROTEIN / Structure 2 Function Project / S2F
Function / homologyTautomerase, MSAD family / Tautomerase enzyme / Macrophage Migration Inhibitory Factor / Macrophage Migration Inhibitory Factor / Tautomerase/MIF superfamily / 2-Layer Sandwich / Alpha Beta / GLUTAMIC ACID / Uncharacterized protein HI_1388.1
Function and homology information
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å
AuthorsLehmann, C. / Pullalarevu, S. / Krajewski, W. / Galkin, A. / Howard, A. / Herzberg, O. / Structure 2 Function Project (S2F)
CitationJournal: To be Published
Title: Structure of the Hypothetical Protein HI1388.1 from Haemophilus influenzae
Authors: Lehmann, C. / Pullalarevu, S. / Krajewski, W. / Galkin, A. / Howard, A. / Herzberg, O.
History
DepositionOct 1, 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 1.3Feb 14, 2024Group: 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: HYPOTHETICAL PROTEIN HI1388.1
B: HYPOTHETICAL PROTEIN HI1388.1
C: HYPOTHETICAL PROTEIN HI1388.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1395
Polymers44,9563
Non-polymers1832
Water6,413356
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7440 Å2
ΔGint-35 kcal/mol
Surface area14650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.150, 115.150, 124.420
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11B-245-

HOH

21C-512-

HOH

31C-520-

HOH

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Components

#1: Protein HYPOTHETICAL PROTEIN HI1388.1


Mass: 14985.425 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: HI1388.1 / Plasmid: PET100 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O86237
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 356 / 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: 2.14 Å3/Da / Density % sol: 46.36 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 50% MPD, 0.1M NACACODYLATE, 0.2M NAGLUTAMATE, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.9724 / Wavelength: 0.9724 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 7, 2002 / Details: MIRROR
RadiationMonochromator: CRYOGENICALLY-COOLED SI(111) DOUBLE-CRYSTAL SYSTEM
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9724 Å / Relative weight: 1
ReflectionResolution: 2.08→19.83 Å / Num. obs: 24983 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.9 % / Biso Wilson estimate: 29.8 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 15.5
Reflection shellResolution: 2.08→2.15 Å / Rmerge(I) obs: 0.305 / Mean I/σ(I) obs: 8.96 / Num. unique all: 24986 / % possible all: 89.6

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Processing

Software
NameClassification
HKL-2000data collection
HKL-2000data reduction
EPMRphasing
RESOLVEmodel building
CNSrefinement
HKL-2000data scaling
RESOLVEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OTF

1otf


Resolution: 2.08→19.83 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.269 1194 -RANDOM
Rwork0.198 ---
obs-24578 99 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Displacement parametersBiso mean: 32.6 Å2
Refinement stepCycle: LAST / Resolution: 2.08→19.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2924 0 11 356 3291
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.021
X-RAY DIFFRACTIONc_angle_deg1.9
LS refinement shellResolution: 2.08→2.17 Å
RfactorNum. reflection% reflection
Rfree0.423 117 -
Rwork0.299 2586 -
obs-2703 89.6 %

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