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- PDB-2je2: Cytochrome P460 from Nitrosomonas europaea - probable nonphysiolo... -

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Basic information

Entry
Database: PDB / ID: 2je2
TitleCytochrome P460 from Nitrosomonas europaea - probable nonphysiological oxidized form
ComponentsCYTOCHROME P460
KeywordsMETAL BINDING PROTEIN / HEME P460 / CYTOCHROME P460 / CROSS-LINKED HEME
Function / homology
Function and homology information


Cytochrome P460 / Cytochrome P460 / Cytochrome P460 superfamily / Cytochrome P460 / Chalcone isomerase / 3-Layer(bba) Sandwich / Alpha Beta
Similarity search - Domain/homology
HEME C / PHOSPHATE ION / Cytochrome P460
Similarity search - Component
Biological speciesNITROSOMONAS EUROPAEA (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsPearson, A.R. / Elmore, B.O. / Yang, C. / Ferrara, J.D. / Hooper, A.B. / Wilmot, C.M.
CitationJournal: Biochemistry / Year: 2007
Title: The Crystal Structure of Cytochrome P460 of Nitrosomonas Europaea Reveals a Novel Cytochrome Fold and Heme-Protein Cross-Link.
Authors: Pearson, A.R. / Elmore, B.O. / Yang, C. / Ferrara, J.D. / Hooper, A.B. / Wilmot, C.M.
History
DepositionJan 13, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _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
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CYTOCHROME P460
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4325
Polymers20,5281
Non-polymers9034
Water2,378132
1
A: CYTOCHROME P460
hetero molecules

A: CYTOCHROME P460
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,86310
Polymers41,0562
Non-polymers1,8078
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
MethodPQS
Unit cell
Length a, b, c (Å)53.256, 53.256, 127.033
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein CYTOCHROME P460


Mass: 20528.113 Da / Num. of mol.: 1 / Fragment: RESIDUES 27-198
Source method: isolated from a genetically manipulated source
Details: PROTEIN-HEME CROSS-LINK FROM NZ OF LYS 70 TO CHA OF HEC 200. PROTEIN-HEME CROSSLINK FROM SG OF CYS 136 TO CAB OF HEC 200. PROTEIN-HEME CROSSLINK FROM SG OF CYS 139 TO CAC OF HEC 200.
Source: (gene. exp.) NITROSOMONAS EUROPAEA (bacteria)
Description: CONTAINS ADDITIONAL N-TERMINAL METHIONINE AND AT THE TERMINUS THE ADDITIONS RESIDUES KLAAALEHHHHHH
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q50927
#2: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsRECOMBINANT PROTEIN CONTAINS ADDITIONAL N-TERMINAL METHIONINE AND C-TERMINAL TAG KLAAALEHHHHHH

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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: 2.6 Å3/Da / Density % sol: 51.1 %
Description: THE STRUCTURE WAS SOLVED BY SAD USING A DATASET COLLECTED AT CR K-ALPHA. PHASED USING SHELX AND SHARP. THE INITIAL MODEL WAS THEN USED TO PHASE THE HIGHER RESOLUTION CU K-ALPHA DATASET.
Crystal growpH: 5.2 / Details: pH 5.20

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: May 5, 2005 / Details: VARIMAX CONFOCAL MAXFLUX
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.69→43 Å / Num. obs: 17631 / % possible obs: 80.9 % / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Biso Wilson estimate: 25.3 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 17.7
Reflection shellResolution: 1.69→1.75 Å / Redundancy: 1.1 % / Rmerge(I) obs: 0.1 / Mean I/σ(I) obs: 2.8 / % possible all: 13.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: INITIAL MODEL FROM SULPHUR SAD STRUCTURE

Resolution: 1.8→43.36 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.937 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.128 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.237 952 5.1 %RANDOM
Rwork0.197 ---
obs0.199 17631 92.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.8→43.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1223 0 58 132 1413
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221336
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6412.0571837
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1075162
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.58624.21157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.82615201
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.394156
X-RAY DIFFRACTIONr_chiral_restr0.1420.2191
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021024
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.270.2663
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.2897
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.296
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1760.253
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1730.223
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0231.5807
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.75621277
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.2833621
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3984.5554
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.345 54
Rwork0.283 783

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