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- PDB-4dil: Flavo Di-iron protein H90N mutant from Thermotoga maritima -

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Basic information

Entry
Database: PDB / ID: 4dil
TitleFlavo Di-iron protein H90N mutant from Thermotoga maritima
ComponentsFLAVOPROTEIN
KeywordsELECTRON TRANSPORT / TM0755 / FLAVOPROTEIN / di-iron protein
Function / homology
Function and homology information


FMN binding / oxidoreductase activity / electron transfer activity / metal ion binding
Similarity search - Function
Rubredoxin-oxygen oxidoreductase / ODP domain / ODP family beta lactamase / Flavodoxin domain / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Flavodoxin ...Rubredoxin-oxygen oxidoreductase / ODP domain / ODP family beta lactamase / Flavodoxin domain / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Flavodoxin / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Flavoprotein-like superfamily / 4-Layer Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
MU-OXO-DIIRON / Flavodoxin-like domain-containing protein
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsFang, H. / Caranto, J.D. / Taylor, A.B. / Hart, P.J. / Kurtz, D.M.
CitationJournal: J.Biol.Inorg.Chem. / Year: 2012
Title: Histidine ligand variants of a flavo-diiron protein: effects on structure and activities.
Authors: Fang, H. / Caranto, J.D. / Mendoza, R. / Taylor, A.B. / Hart, P.J. / Kurtz, D.M.
History
DepositionJan 31, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 2, 2013Group: Database references
Revision 1.2Oct 8, 2014Group: Structure summary
Revision 1.3Sep 13, 2023Group: 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_auth_seq_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FLAVOPROTEIN
B: FLAVOPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,9037
Polymers93,5412
Non-polymers3625
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5040 Å2
ΔGint-94 kcal/mol
Surface area29880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.647, 91.939, 86.341
Angle α, β, γ (deg.)90.00, 96.79, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein FLAVOPROTEIN


Mass: 46770.695 Da / Num. of mol.: 2 / Mutation: H90N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM0755, TM_0755 / Plasmid: pMH1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WZL4
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-FEO / MU-OXO-DIIRON


Mass: 127.689 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 2.3 Å3/Da / Density % sol: 46.58 %
Crystal growTemperature: 277 K / pH: 4
Details: 0.1 M sodium acetate, 40% MPD, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Mar 24, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 57555 / % possible obs: 99.8 % / Redundancy: 6.6 % / Biso Wilson estimate: 36.6 Å2 / Rsym value: 0.072 / Net I/σ(I): 23
Reflection shellResolution: 2→2.07 Å / Redundancy: 6 % / Mean I/σ(I) obs: 3.4 / Rsym value: 0.508 / % possible all: 99.8

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VME

1vme


Resolution: 2→28.86 Å / SU ML: 0.21 / Isotropic thermal model: isotropic / σ(F): 1.33 / Phase error: 26.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.235 2875 5 %
Rwork0.198 --
obs0.2 57492 99.4 %
Solvent computationShrinkage radii: 1.24 Å / VDW probe radii: 1.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 23.63 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 37.5 Å2
Baniso -1Baniso -2Baniso -3
1-7.7788 Å20 Å2-13.7628 Å2
2--2.9008 Å20 Å2
3---9.3103 Å2
Refinement stepCycle: LAST / Resolution: 2→28.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6339 0 9 185 6533
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076572
X-RAY DIFFRACTIONf_angle_d1.098897
X-RAY DIFFRACTIONf_dihedral_angle_d15.1582456
X-RAY DIFFRACTIONf_chiral_restr0.072989
X-RAY DIFFRACTIONf_plane_restr0.0051119
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9937-2.02630.36521260.29662398X-RAY DIFFRACTION92
2.0263-2.06130.33711370.26872601X-RAY DIFFRACTION100
2.0613-2.09870.34261380.25462623X-RAY DIFFRACTION100
2.0987-2.13910.30821370.24522588X-RAY DIFFRACTION100
2.1391-2.18270.28981380.2362621X-RAY DIFFRACTION100
2.1827-2.23020.29961350.22292580X-RAY DIFFRACTION100
2.2302-2.2820.27041390.22682638X-RAY DIFFRACTION100
2.282-2.33910.28031350.20552576X-RAY DIFFRACTION100
2.3391-2.40230.26241380.20952595X-RAY DIFFRACTION100
2.4023-2.4730.26511390.20752647X-RAY DIFFRACTION100
2.473-2.55270.28961360.22252585X-RAY DIFFRACTION100
2.5527-2.64390.31360.22282583X-RAY DIFFRACTION100
2.6439-2.74970.22131390.22492642X-RAY DIFFRACTION100
2.7497-2.87470.25371380.21732614X-RAY DIFFRACTION100
2.8747-3.02610.24741370.22222609X-RAY DIFFRACTION100
3.0261-3.21550.26291380.2132616X-RAY DIFFRACTION100
3.2155-3.46340.23411370.20752612X-RAY DIFFRACTION100
3.4634-3.81120.23161380.1872612X-RAY DIFFRACTION100
3.8112-4.36110.17921360.16592592X-RAY DIFFRACTION99
4.3611-5.48830.18541370.15642620X-RAY DIFFRACTION98
5.4883-28.86110.20421410.18262665X-RAY DIFFRACTION100

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