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- PDB-1lkp: Crystal structure of Desulfovibrio vulgaris rubrerythrin all-iron... -

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Basic information

Entry
Database: PDB / ID: 1lkp
TitleCrystal structure of Desulfovibrio vulgaris rubrerythrin all-iron(II) form, azide adduct
ComponentsRubrerythrin
KeywordsELECTRON TRANSPORT / Rubrerythrin / reduced form / azide adduct / diiron / four-helix bundle / rubredoxin-like
Function / homology
Function and homology information


oxidoreductase activity / iron ion binding / cytoplasm
Similarity search - Function
: / : / Rubrerythrin, rubredoxin-like domain / Rubrerythrin, diiron-binding domain / Rubrerythrin / Rubrerythrin, domain 2 - #10 / Rubredoxin-like domain / Rubredoxin-like domain profile. / Rubrerythrin, domain 2 / Ferritin, core subunit, four-helix bundle ...: / : / Rubrerythrin, rubredoxin-like domain / Rubrerythrin, diiron-binding domain / Rubrerythrin / Rubrerythrin, domain 2 - #10 / Rubredoxin-like domain / Rubredoxin-like domain profile. / Rubrerythrin, domain 2 / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin-like / Single Sheet / Ferritin-like superfamily / Up-down Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
AZIDE ION / : / Rubrerythrin
Similarity search - Component
Biological speciesDesulfovibrio vulgaris (bacteria)
MethodX-RAY DIFFRACTION / Difference Fourier analysis / Resolution: 1.64 Å
AuthorsJin, S. / Kurtz Jr., D.M. / Liu, Z.J. / Rose, J. / Wang, B.C.
CitationJournal: J.Am.Chem.Soc. / Year: 2002
Title: X-ray Crystal Structures of Reduced Rubrerythrin and its Azide Adduct: A Structure-Based Mechanism for a Non-Heme Diiron Peroxidase
Authors: Jin, S. / Kurtz Jr., D.M. / Liu, Z.J. / Rose, J. / Wang, B.C.
History
DepositionApr 25, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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_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
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rubrerythrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8296
Polymers21,5771
Non-polymers2525
Water4,720262
1
A: Rubrerythrin
hetero molecules

A: Rubrerythrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,65812
Polymers43,1552
Non-polymers50310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area4490 Å2
ΔGint-68 kcal/mol
Surface area17890 Å2
MethodPISA
2
A: Rubrerythrin
hetero molecules

A: Rubrerythrin
hetero molecules

A: Rubrerythrin
hetero molecules

A: Rubrerythrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,31524
Polymers86,3094
Non-polymers1,00620
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
Buried area14840 Å2
ΔGint-174 kcal/mol
Surface area29910 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)48.344, 80.092, 100.168
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Rubrerythrin


Mass: 21577.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: all-iron (II) form / Source: (gene. exp.) Desulfovibrio vulgaris (bacteria) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): 'BL21(DE3) / References: UniProt: P24931
#2: Chemical ChemComp-AZI / AZIDE ION


Mass: 42.020 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: N3
#3: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 262 / 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: 2.25 Å3/Da / Density % sol: 45.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: PEG 1450, MOPS, Sodium Azide, Sodium Dithionite, NADH, BenC, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 8 / Details: deMare, F., (1996) Nature Struct. Biol., 3, 539.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.1 MTRIZMA hydrochloride1reservoir
215 %PEG14501reservoir
312 %glycerol1reservoir

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 19, 2000 / Details: Confocal Maxflux Optics
RadiationMonochromator: Confocal Maxflux Optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.64→50 Å / Num. all: 21668 / Num. obs: 21668 / % possible obs: 89.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 18.9 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 46.5
Reflection shellResolution: 1.64→1.7 Å / Redundancy: 1.1 % / Rmerge(I) obs: 0.186 / Mean I/σ(I) obs: 5.1 / Num. unique all: 1098 / % possible all: 46.2
Reflection
*PLUS
Lowest resolution: 50 Å / Num. obs: 21509 / % possible obs: 88.6 % / Num. measured all: 133046 / Rmerge(I) obs: 0.058
Reflection shell
*PLUS
Rmerge(I) obs: 0.186

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: Difference Fourier analysis
Starting model: Rubrerythrin all-iron(II) form

Resolution: 1.64→23.37 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 395688.3 / 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
Rfree0.202 1700 7.9 %RANDOM
Rwork0.178 ---
all0.18 21668 --
obs0.178 21509 88.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 33.8298 Å2 / ksol: 0.330348 e/Å3
Displacement parametersBiso mean: 17.5 Å2
Baniso -1Baniso -2Baniso -3
1-6.43 Å20 Å20 Å2
2---3.2 Å20 Å2
3----3.23 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.11 Å0.05 Å
Refinement stepCycle: LAST / Resolution: 1.64→23.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1514 0 9 262 1785
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.73
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.021.5
X-RAY DIFFRACTIONc_mcangle_it1.482
X-RAY DIFFRACTIONc_scbond_it2.042
X-RAY DIFFRACTIONc_scangle_it3.062.5
LS refinement shellResolution: 1.64→1.74 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.303 159 7.8 %
Rwork0.298 1869 -
obs-2028 51.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAM
X-RAY DIFFRACTION3WATER_REP.PARAM
X-RAY DIFFRACTION4CIS_PEPTIDE-RE-12-19.PARAM
X-RAY DIFFRACTION5NNN_XPLOR_PAR.PARAM
Refinement
*PLUS
Rfactor all: 0.18 / Rfactor obs: 0.178 / Rfactor Rfree: 0.2023 / Rfactor Rwork: 0.178
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.73
LS refinement shell
*PLUS
Rfactor Rfree: 0.303 / Rfactor Rwork: 0.298

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