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- PDB-1gvh: The X-ray structure of ferric Escherichia coli flavohemoglobin re... -

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Basic information

Entry
Database: PDB / ID: 1gvh
TitleThe X-ray structure of ferric Escherichia coli flavohemoglobin reveals an unespected geometry of the distal heme pocket
ComponentsFLAVOHEMOPROTEIN
KeywordsOXIDOREDUCTASE / NADP / HEME / FLAVOPROTEIN / FAD / IRON TRANSPOR
Function / homology
Function and homology information


nitric oxide dioxygenase / hydroperoxide reductase activity / cellular response to nitrosative stress / nitric oxide dioxygenase NAD(P)H activity / nitric oxide catabolic process / response to nitrosative stress / FAD binding / fatty acid binding / oxygen carrier activity / response to toxic substance ...nitric oxide dioxygenase / hydroperoxide reductase activity / cellular response to nitrosative stress / nitric oxide dioxygenase NAD(P)H activity / nitric oxide catabolic process / response to nitrosative stress / FAD binding / fatty acid binding / oxygen carrier activity / response to toxic substance / oxygen binding / heme binding / metal ion binding / cytoplasm
Similarity search - Function
Flavohemoprotein / Flavoprotein pyridine nucleotide cytochrome reductase-like, FAD-binding domain / Oxidoreductase FAD-binding domain / Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module / Translation factors / Globin/Protoglobin / Elongation Factor Tu (Ef-tu); domain 3 / Oxidoreductase FAD/NAD(P)-binding / Oxidoreductase NAD-binding domain / FAD-binding domain, ferredoxin reductase-type ...Flavohemoprotein / Flavoprotein pyridine nucleotide cytochrome reductase-like, FAD-binding domain / Oxidoreductase FAD-binding domain / Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module / Translation factors / Globin/Protoglobin / Elongation Factor Tu (Ef-tu); domain 3 / Oxidoreductase FAD/NAD(P)-binding / Oxidoreductase NAD-binding domain / FAD-binding domain, ferredoxin reductase-type / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / Ferredoxin reductase-type FAD binding domain profile. / Riboflavin synthase-like beta-barrel / Globins / Globin family profile. / Globin-like / Globin / Globin / Globin-like superfamily / Beta Barrel / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / PROTOPORPHYRIN IX CONTAINING FE / Flavohemoprotein
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.19 Å
AuthorsIlari, A. / Johnson, K.A. / Bonamore, A. / Farina, A. / Boffi, A.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: The X-Ray Structure of Ferric Escherichia Coli Flavohemoglobin Reveals an Unexpected Geometry of the Distal Heme Pocket
Authors: Ilari, A. / Bonamore, A. / Farina, A. / Johnson, K.A. / Boffi, A.
History
DepositionFeb 13, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 6, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FLAVOHEMOPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4006
Polymers43,9161
Non-polymers1,4835
Water3,441191
1
A: FLAVOHEMOPROTEIN
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)544,79972
Polymers526,99712
Non-polymers17,80260
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555y,-x+y,z1
crystal symmetry operation6_555x-y,x,z1
crystal symmetry operation12_559x,x-y,-z+41
crystal symmetry operation8_559x-y,-y,-z+41
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation7_559y,x,-z+41
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation10_559-y,-x,-z+41
crystal symmetry operation4_555-x,-y,z1
crystal symmetry operation11_559-x+y,y,-z+41
crystal symmetry operation9_559-x,-x+y,-z+41
MethodPQS
Unit cell
Length a, b, c (Å)164.860, 164.860, 53.460
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number177
Space group name H-MP622

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Components

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Protein , 1 types, 1 molecules A

#1: Protein FLAVOHEMOPROTEIN / FLAVOHEMOGLOBIN / DIHYDROPTERIDINE REDUCTASE / HEMOGLOBIN-LIKE PROTEIN / DIHYDROPTERIDINE REDUCTASE ...FLAVOHEMOGLOBIN / DIHYDROPTERIDINE REDUCTASE / HEMOGLOBIN-LIKE PROTEIN / DIHYDROPTERIDINE REDUCTASE / FERRISIDEROPHORE REDUCTASE B / NITRIC OXIDE DIOXYGENASE / NOD


Mass: 43916.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / References: UniProt: P24232, 1.6.99.7

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Non-polymers , 5 types, 196 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 191 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.49 %
Crystal growpH: 5.1
Details: SODIUM ACETATE 0.1 M PH 5.1, PEG 3350 21-26%, NACL 0.2 M
Crystal grow
*PLUS
Temperature: 25 ℃ / Method: vapor diffusion, sitting drop / PH range low: 5.3 / PH range high: 5.1
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
122 mg/mlprotein1drop
20.1 Msodium acetate1reservoirpH5.1-5.3
321-26 %PEG33501reservoir
40.2 M1reservoirNaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.19→25 Å / Num. obs: 22448 / % possible obs: 99.5 % / Redundancy: 11 % / Rmerge(I) obs: 0.09
Reflection
*PLUS
Lowest resolution: 25 Å / Rmerge(I) obs: 0.09

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Processing

Software
NameVersionClassification
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2.19→25 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.247 --
Rwork0.187 --
obs0.187 22443 99.39 %
Refinement stepCycle: LAST / Resolution: 2.19→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3097 0 99 191 3387
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.8
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d4.19
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROLSQ.PROTTOPH19X_HEME.PRO
X-RAY DIFFRACTION2PARAM19X.HEMETOPOL.FAD
X-RAY DIFFRACTION3PARAM.FADTOPH19.SOL
X-RAY DIFFRACTION4PARAM19.SOLV
Refinement
*PLUS
Lowest resolution: 25 Å / Rfactor Rwork: 0.188
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.801
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.397
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg4.19

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