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- PDB-3wfx: Crystal Structure of the Imidazole-Bound Form of the HGbRL's Glob... -

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Basic information

Entry
Database: PDB / ID: 3wfx
TitleCrystal Structure of the Imidazole-Bound Form of the HGbRL's Globin Domain
ComponentsHemoglobin-like flavoprotein fused to Roadblock/LC7 domain
KeywordsOXYGEN TRANSPORT / Globin / Signalling / Imidazole
Function / homology
Function and homology information


nitric oxide dioxygenase NAD(P)H activity / cellular response to nitrosative stress / nitric oxide catabolic process / FAD binding / oxygen carrier activity / oxygen binding / heme binding / metal ion binding
Similarity search - Function
Globin/Protoglobin / Globins / Globin domain profile. / Globin-like / Globin / Globin / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / HEXANE-1,6-DIOL / IMIDAZOLE / Hemoglobin-like flavoprotein fused to Roadblock/LC7 domain
Similarity search - Component
Biological speciesMethylacidiphilum infernorum (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsTeh, A.H.
CitationJournal: Sci Rep / Year: 2015
Title: Open and Lys-His Hexacoordinated Closed Structures of a Globin with Swapped Proximal and Distal Sites.
Authors: Teh, A.H. / Saito, J.A. / Najimudin, N. / Alam, M.
History
DepositionJul 24, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 6, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2020Group: Database references / Derived calculations
Category: citation / pdbx_struct_conn_angle ...citation / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr3_auth_asym_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_asym_id / _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_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Hemoglobin-like flavoprotein fused to Roadblock/LC7 domain
B: Hemoglobin-like flavoprotein fused to Roadblock/LC7 domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,20512
Polymers33,1252
Non-polymers2,08010
Water2,612145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10160 Å2
ΔGint-77 kcal/mol
Surface area14900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.580, 44.330, 81.880
Angle α, β, γ (deg.)90.00, 119.68, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Hemoglobin-like flavoprotein fused to Roadblock/LC7 domain


Mass: 16562.338 Da / Num. of mol.: 2 / Fragment: N-terminal Globin Domain, UNP residues 1-133
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylacidiphilum infernorum (bacteria)
Strain: V4 / Gene: hmp, Minf_1089 / Plasmid: pET-3a / Production host: Escherichia coli (E. coli) / References: UniProt: B3DUZ1
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-HEZ / HEXANE-1,6-DIOL


Mass: 118.174 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H14O2
#4: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 2.35 Å3/Da / Density % sol: 47.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 3.5M 1,6-hexanediol, 0.1M sodium citrate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 19, 2011
RadiationMonochromator: VARIMAX HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.94→30 Å / Num. obs: 21708 / % possible obs: 94.31 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 13.89
Reflection shellResolution: 1.94→1.99 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.307 / Mean I/σ(I) obs: 2.99 / Num. unique all: 1661 / % possible all: 99.4

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
PHENIX1.8.2refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3S1I

3s1i


Resolution: 1.94→27.232 Å / Occupancy max: 1 / Occupancy min: 0.39 / SU ML: 0.21 / σ(F): 2 / Phase error: 24.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2339 1086 5 %RANDOM
Rwork0.1832 ---
all0.1857 21703 --
obs0.1857 21703 94.29 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 63.28 Å2 / Biso mean: 25.8731 Å2 / Biso min: 7.34 Å2
Refinement stepCycle: LAST / Resolution: 1.94→27.232 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2280 0 144 145 2569
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072547
X-RAY DIFFRACTIONf_angle_d1.0273450
X-RAY DIFFRACTIONf_dihedral_angle_d20.23980
X-RAY DIFFRACTIONf_chiral_restr0.07353
X-RAY DIFFRACTIONf_plane_restr0.005418
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.94-2.02820.28251410.1982677281899
2.0282-2.13510.28841260.21542395252188
2.1351-2.26890.27771230.21182338246186
2.2689-2.44390.27451400.19532648278897
2.4439-2.68970.24111400.18342674281498
2.6897-3.07840.23971410.18492672281398
3.0784-3.87670.22361390.17432638277796
3.8767-27.23430.19781360.17082575271191

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