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- PDB-4dik: Flavo Di-iron protein H90A mutant from Thermotoga maritima -

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Basic information

Entry
Database: PDB / ID: 4dik
TitleFlavo Di-iron protein H90A mutant from Thermotoga maritima
ComponentsFLAVOPROTEIN
KeywordsELECTRON TRANSPORT / TM0755 / FLAVOPROTEIN / di-iron protein
Function / homology
Function and homology information


FMN binding / electron transfer activity / oxidoreductase 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: 1.75 Å
AuthorsFang, H. / Caranto, J.D. / Taylor, A.B. / Hart, P.J. / Kurtz Jr., 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 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
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.ptnr2_label_atom_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)93,8177
Polymers93,4552
Non-polymers3625
Water7,746430
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-86 kcal/mol
Surface area31070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.219, 96.007, 90.331
Angle α, β, γ (deg.)90.00, 95.81, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein FLAVOPROTEIN


Mass: 46727.668 Da / Num. of mol.: 2 / Mutation: H90A
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.: 430 / 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: 2.55 Å3/Da / Density % sol: 51.74 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 0.1 M sodium acetate, 45% 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 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Aug 10, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.75→30 Å / Num. obs: 94279 / % possible obs: 99.7 % / Redundancy: 3.5 % / Biso Wilson estimate: 28.2 Å2 / Rsym value: 0.041 / Net I/σ(I): 24.5
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 9411 / Rsym value: 0.486 / % possible all: 100

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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: 1.75→29.129 Å / SU ML: 0.22 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1.44 / Phase error: 23.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2153 4711 5 %random
Rwork0.1913 ---
obs0.1925 94191 99.32 %-
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 32.9 Å2
Baniso -1Baniso -2Baniso -3
1-1.3889 Å20 Å2-6.7777 Å2
2--5.1878 Å20 Å2
3----3.6114 Å2
Refinement stepCycle: LAST / Resolution: 1.75→29.129 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6450 0 9 430 6889
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096790
X-RAY DIFFRACTIONf_angle_d1.1859215
X-RAY DIFFRACTIONf_dihedral_angle_d12.3082552
X-RAY DIFFRACTIONf_chiral_restr0.0791017
X-RAY DIFFRACTIONf_plane_restr0.0061166
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.747-1.76680.34951440.30762718X-RAY DIFFRACTION91
1.7668-1.78760.27481570.28883007X-RAY DIFFRACTION100
1.7876-1.80940.30871570.26842977X-RAY DIFFRACTION100
1.8094-1.83230.3021590.25553008X-RAY DIFFRACTION100
1.8323-1.85640.28751560.24572981X-RAY DIFFRACTION100
1.8564-1.88190.30271580.23913007X-RAY DIFFRACTION100
1.8819-1.90870.28741580.23663002X-RAY DIFFRACTION100
1.9087-1.93720.28521560.21612937X-RAY DIFFRACTION100
1.9372-1.96750.26441590.20853021X-RAY DIFFRACTION100
1.9675-1.99970.22711550.20172951X-RAY DIFFRACTION100
1.9997-2.03420.24251570.19432981X-RAY DIFFRACTION100
2.0342-2.07120.24741580.19732994X-RAY DIFFRACTION100
2.0712-2.1110.2581590.19163025X-RAY DIFFRACTION100
2.111-2.15410.2061560.19522972X-RAY DIFFRACTION100
2.1541-2.20090.25461590.18943008X-RAY DIFFRACTION100
2.2009-2.25210.23921580.19633004X-RAY DIFFRACTION100
2.2521-2.30840.24881580.19283000X-RAY DIFFRACTION100
2.3084-2.37080.23821570.19822975X-RAY DIFFRACTION100
2.3708-2.44050.21931580.19493013X-RAY DIFFRACTION100
2.4405-2.51920.21821580.19883018X-RAY DIFFRACTION100
2.5192-2.60920.23141560.19992955X-RAY DIFFRACTION100
2.6092-2.71360.24651570.20392992X-RAY DIFFRACTION100
2.7136-2.8370.2711590.2073010X-RAY DIFFRACTION100
2.837-2.98650.22881580.20193013X-RAY DIFFRACTION100
2.9865-3.17340.22251590.19092996X-RAY DIFFRACTION100
3.1734-3.4180.20181580.18882998X-RAY DIFFRACTION100
3.418-3.76140.191580.17923001X-RAY DIFFRACTION99
3.7614-4.30410.17321540.16412937X-RAY DIFFRACTION97
4.3041-5.41710.17741540.1532920X-RAY DIFFRACTION96
5.4171-29.13320.17551610.19443059X-RAY DIFFRACTION99

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