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- PDB-2gqf: Crystal structure of flavoprotein HI0933 from Haemophilus influen... -

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Basic information

Entry
Database: PDB / ID: 2gqf
TitleCrystal structure of flavoprotein HI0933 from Haemophilus influenzae Rd
ComponentsHypothetical protein HI0933
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / FAD-utilizing protein / flavoprotein / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


Oxidoreductases; Acting on the CH-CH group of donors; With NAD+ or NADP+ as acceptor
Similarity search - Function
HI0933 insert domain-like / 3-Dehydro-bile acid delta(4,6)-reductase-like / HI0933-like insert domain superfamily / : / HI0933-like protein Rossmann domain / HI0933-like protein barrel and H2TH domain / Translation factors / Elongation Factor Tu (Ef-tu); domain 3 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain ...HI0933 insert domain-like / 3-Dehydro-bile acid delta(4,6)-reductase-like / HI0933-like insert domain superfamily / : / HI0933-like protein Rossmann domain / HI0933-like protein barrel and H2TH domain / Translation factors / Elongation Factor Tu (Ef-tu); domain 3 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / Helicase, Ruva Protein; domain 3 / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Ribosomal RNA dihydrouridine synthase
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsMulichak, A.M. / Patskovsky, Y. / Keefe, L.J. / Almo, S.C. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of hypothetical flavoprotein HI0933 from Haemophilus influenzae Rd.
Authors: Mulichak, A.M. / Patskovsky, Y. / Keefe, L.J. / Almo, S.C.
History
DepositionApr 20, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / struct_conn ...audit_author / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag ..._audit_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypothetical protein HI0933
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7283
Polymers44,8461
Non-polymers8822
Water3,531196
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Hypothetical protein HI0933
hetero molecules

A: Hypothetical protein HI0933
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,4556
Polymers89,6922
Non-polymers1,7634
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_655-x+y+1,y,-z1
Buried area4810 Å2
ΔGint-61 kcal/mol
Surface area31670 Å2
MethodPISA
3
A: Hypothetical protein HI0933
hetero molecules

A: Hypothetical protein HI0933
hetero molecules

A: Hypothetical protein HI0933
hetero molecules

A: Hypothetical protein HI0933
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,91112
Polymers179,3844
Non-polymers3,5268
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
crystal symmetry operation7_554y,x,-z-1/31
crystal symmetry operation10_664-y+1,-x+1,-z-1/31
MethodPQS
Unit cell
Length a, b, c (Å)160.730, 160.730, 100.790
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-402-

SO4

21A-441-

HOH

31A-506-

HOH

41A-556-

HOH

DetailsThe biological assembly is a monomer.

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Components

#1: Protein Hypothetical protein HI0933


Mass: 44846.066 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: HI0933 / Production host: Escherichia coli (E. coli) / References: UniProt: P44941
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 4.19 Å3/Da / Density % sol: 70.64 %
Crystal growTemperature: 298 K / pH: 5.5
Details: ammonium sulfate, 0.1M Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 5.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.979228
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 9, 2006
RadiationMonochromator: SI 111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979228 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 40093 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 11.7 % / Rsym value: 0.11
Reflection shellResolution: 2.75→2.8 Å / % possible all: 100

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Processing

Software
NameClassification
JDirectordata collection
HKL-2000data reduction
CNSrefinement
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: SAD / Resolution: 2.7→30 Å / Isotropic thermal model: ISOTROPIC / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.233 1952 -RANDOM
Rwork0.192 ---
obs0.192 38390 96 %-
all-40010 --
Refinement stepCycle: LAST / Resolution: 2.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3104 0 58 196 3358
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2ION.PARAM
X-RAY DIFFRACTION3DNA-RNA_REP.PARAM
X-RAY DIFFRACTION4WATER_REP.PARAM
X-RAY DIFFRACTION5LIGAND.PARAM

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