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- PDB-1cqx: Crystal structure of the flavohemoglobin from Alcaligenes eutroph... -

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Basic information

Entry
Database: PDB / ID: 1cqx
TitleCrystal structure of the flavohemoglobin from Alcaligenes eutrophus at 1.75 A resolution
ComponentsFLAVOHEMOPROTEIN
KeywordsLIPID BINDING PROTEIN / GLOBIN FOLD / SIX-STRANDED ANTIPARALLEL BETA SHEET / HELIX-FLANKED FIVE-STRANDED PARALLEL BETA SHEET
Function / homology
Function and homology information


nitric oxide dioxygenase / nitric oxide dioxygenase NAD(P)H activity / cellular response to nitrosative stress / nitric oxide catabolic process / FAD binding / oxygen carrier activity / oxygen binding / response to toxic substance / 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 domain 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
Chem-DGG / FLAVIN-ADENINE DINUCLEOTIDE / PROTOPORPHYRIN IX CONTAINING FE / Flavohemoprotein
Similarity search - Component
Biological speciesCupriavidus necator (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.75 Å
AuthorsErmler, U. / Siddiqui, R.A. / Cramm, R. / Friedrich, B.
Citation
Journal: EMBO J. / Year: 1995
Title: Crystal structure of the flavohemoglobin from Alcaligenes eutrophus at 1.75 A resolution.
Authors: Ermler, U. / Siddiqui, R.A. / Cramm, R. / Friedrich, B.
#1: Journal: Eur.J.Biochem. / Year: 1999
Title: Phospholipid bound to the flavohemoprotein from alcaligenes eutrophus
Authors: Ollesch, G. / Kaunzinger, A. / Juchelka, D. / Schubert-Zsilavecz, M. / Ermler, U.
History
DepositionAug 12, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 / _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

Downloads & links

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Assembly

Deposited unit
A: FLAVOHEMOPROTEIN
B: FLAVOHEMOPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,9899
Polymers89,6922
Non-polymers4,2977
Water10,467581
1
A: FLAVOHEMOPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0065
Polymers44,8461
Non-polymers2,1604
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: FLAVOHEMOPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9834
Polymers44,8461
Non-polymers2,1373
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10350 Å2
ΔGint-105 kcal/mol
Surface area33880 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)52.200, 85.800, 103.900
Angle α, β, γ (deg.)90.00, 81.80, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein FLAVOHEMOPROTEIN


Mass: 44845.895 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Cupriavidus necator (bacteria)
Keywords: COMPLEXED WITH HEME, FLAVIN-ADENINE DINUCLEOTIDE AND PHOSPHO LIPID
References: UniProt: P39662

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Non-polymers , 5 types, 588 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#5: Chemical ChemComp-DGG / 1-[GLYCEROLYLPHOSPHONYL]-2-[8-(2-HEXYL-CYCLOPROPYL)-OCTANAL-1-YL]-3-[HEXADECANAL-1-YL]-GLYCEROL


Mass: 734.981 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C39H75O10P
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 581 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52.07 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: protein solution: TRIS, potassium chloride, DTT, plus precipitant; precipitant: PEG 3350, sodium chloride, sodium citrate, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 281K
Crystal grow
*PLUS
pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
20.02 MTris-HCl1drop
30.01 M1dropKCl
42 mMdithiothreitol1drop
514 %PEG33501reservoir
60.2 M1reservoirNaCl
70.05 Msodium citrate1reservoir

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 1, 1993
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 196672 / % possible obs: 90.5 % / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Biso Wilson estimate: 19.9 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 8.1
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.151 / Num. unique all: 8118 / % possible all: 62.7
Reflection shell
*PLUS
% possible obs: 62.7 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
ROTAVATAdata reduction
Agrovatadata reduction
MLPHAREphasing
X-PLORrefinement
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
RefinementResolution: 1.75→10 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 29433623.09 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.215 4066 5 %RANDOM
Rwork0.182 ---
obs-80753 89.7 %-
Displacement parametersBiso mean: 28.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.84 Å20 Å20.53 Å2
2---0.58 Å20 Å2
3----0.26 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 1.75→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6316 0 283 581 7180
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_improper_angle_d1.53
X-RAY DIFFRACTIONc_mcbond_it1.31.5
X-RAY DIFFRACTIONc_mcangle_it2.182
X-RAY DIFFRACTIONc_scbond_it24.22
X-RAY DIFFRACTIONc_scangle_it16.252.5
LS refinement shellResolution: 1.75→1.86 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.254 433 5 %
Rwork0.257 8162 -
obs--56.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAPROTEIN.TOP
X-RAY DIFFRACTION2FAHE.PARAFAHELI.TOP
X-RAY DIFFRACTION3WATER_REP.PARAWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d
X-RAY DIFFRACTIONx_angle_deg
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.6
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.53
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scangle_it

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