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- PDB-1uyu: Xenon COMPLEX OF wildtype P450CAM FROM PSEUDOMONAS PUTIDA -

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Basic information

Entry
Database: PDB / ID: 1uyu
TitleXenon COMPLEX OF wildtype P450CAM FROM PSEUDOMONAS PUTIDA
ComponentsCYTOCHROME P450-CAM
KeywordsOXIDOREDUCTASE / MONO-OXYGENASE / HEME / ELECTRON TRANSPORT
Function / homology
Function and homology information


camphor 5-monooxygenase / camphor 5-monooxygenase activity / (+)-camphor catabolic process / cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic process / iron ion binding / heme binding / cytoplasm
Similarity search - Function
Cytochrome P450, B-class / Cytochrome p450 / Cytochrome P450 / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
CAMPHOR / PROTOPORPHYRIN IX CONTAINING FE / : / XENON / Camphor 5-monooxygenase
Similarity search - Component
Biological speciesPSEUDOMONAS PUTIDA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWade, R.C. / Winn, P.J. / Schlichting, I. / Sudarko, X.
Citation
Journal: J.Inorg.Biochem. / Year: 2004
Title: A Survey of Active Site Access Channels in Cytochromes P450
Authors: Wade, R.C. / Winn, P.J. / Schlichting, I.
#1: Journal: Annu.Rev.Biochem. / Year: 2004
Title: Structural Aspects of Ligand Binding to and Electron Transfer in Bacterial and Fungal P450S
Authors: Pylypenko, O. / Schlichting, I.
#2: Journal: J.Mol.Biol. / Year: 1987
Title: High-Resolution Crystal Structure of Cytochrome P450Cam
Authors: Poulos, T.L. / Finzel, B.C. / Howard, A.J.
History
DepositionMar 2, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 7, 2005Provider: repository / Type: Initial release
Revision 1.1Aug 22, 2012Group: Database references / Other ...Database references / Other / Structure summary / Version format compliance
Revision 1.2Apr 3, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.3Dec 13, 2023Group: 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 / 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_database_status.status_code_sf / _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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CYTOCHROME P450-CAM
B: CYTOCHROME P450-CAM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,88117
Polymers93,1762
Non-polymers2,70515
Water8,143452
1
A: CYTOCHROME P450-CAM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9218
Polymers46,5881
Non-polymers1,3337
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: CYTOCHROME P450-CAM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9609
Polymers46,5881
Non-polymers1,3728
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)67.200, 62.300, 95.300
Angle α, β, γ (deg.)90.00, 90.50, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein CYTOCHROME P450-CAM


Mass: 46587.895 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: HEME ATTACHED VIA CYS357, XENON BOUND IN CAVITIES / Source: (gene. exp.) PSEUDOMONAS PUTIDA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P00183

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Non-polymers , 5 types, 467 molecules

#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-CAM / CAMPHOR


Mass: 152.233 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16O
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#5: Chemical
ChemComp-XE / XENON


Mass: 131.293 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Xe
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 452 / 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: 2.14 Å3/Da / Density % sol: 42.55 %
Description: A CRYOCOOLED, LOOP MOUNTED P450 CRYSTAL CONTAINING CAMPHOR AND HEME-BOUND CYANIDE (NO CYANIDE IN THE CRYOPROTECTANT CONTAINING 20% GLYCEROL) WAS WARMED UP QUICKLY AND MOUNTED IN A HOME- ...Description: A CRYOCOOLED, LOOP MOUNTED P450 CRYSTAL CONTAINING CAMPHOR AND HEME-BOUND CYANIDE (NO CYANIDE IN THE CRYOPROTECTANT CONTAINING 20% GLYCEROL) WAS WARMED UP QUICKLY AND MOUNTED IN A HOME-BUILT PRESSURE CELL. THE CRYSTAL WAS EXPOSED FOR 3 MIN. TO 7 BAR XENON AT 2 DEG. C SUBSEQUENTLY, THE CRYSTAL WAS FLASH COOLED IN LIQUID NITROGEN.
Crystal growTemperature: 275 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: CRYSTALS WERE GROWN USING THE SITTING DROP GEOMETRY AT 2 DEG. C. 5 UL OF 30 MG/ML P450 IN 50 MM TRIS HCL, 250 MM KCL, 0.5 MM CAMPHOR WERE MIXED WITH AN EQUAL VOLUME OF THE RESERVOIR SOLUTION ...Details: CRYSTALS WERE GROWN USING THE SITTING DROP GEOMETRY AT 2 DEG. C. 5 UL OF 30 MG/ML P450 IN 50 MM TRIS HCL, 250 MM KCL, 0.5 MM CAMPHOR WERE MIXED WITH AN EQUAL VOLUME OF THE RESERVOIR SOLUTION (27-30% PEG 4000, 100 MM DTE, SAME BUFFER AS PROTEIN)., pH 7.40

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Type: ESRF / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Details: MIRRORS
RadiationMonochromator: MONO / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2→19 Å / Num. obs: 53282 / % possible obs: 99.7 % / Redundancy: 3.82 % / Biso Wilson estimate: 32.91 Å2 / Rmerge(I) obs: 0.121 / Net I/σ(I): 9.3
Reflection shellResolution: 2→2.1 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.483 / Mean I/σ(I) obs: 4.2 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DZ8

1dz8


Resolution: 2→19.84 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.925 / SU B: 4.249 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.214 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. N-TERMINUS IS DISORDERED
RfactorNum. reflection% reflectionSelection details
Rfree0.236 2663 5 %RANDOM
Rwork0.187 ---
obs0.19 50618 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 31.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å20 Å20.77 Å2
2---0.15 Å20 Å2
3----0.29 Å2
Refinement stepCycle: LAST / Resolution: 2→19.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6406 0 119 452 6977
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0216756
X-RAY DIFFRACTIONr_bond_other_d0.0020.026118
X-RAY DIFFRACTIONr_angle_refined_deg1.4212.0019225
X-RAY DIFFRACTIONr_angle_other_deg0.971314302
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6715813
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0810.2985
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027482
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021320
X-RAY DIFFRACTIONr_nbd_refined0.2170.21530
X-RAY DIFFRACTIONr_nbd_other0.2320.27316
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0860.23729
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1960.2418
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.20.29
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1370.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2710.279
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.220.227
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6371.54081
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.23726629
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.90532675
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.1844.52586
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: 2→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.268 193
Rwork0.21 3666

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