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- PDB-3p3l: Crystal Structure of the Cytochrome P450 monooxygenase AurH (wild... -

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Basic information

Entry
Database: PDB / ID: 3p3l
TitleCrystal Structure of the Cytochrome P450 monooxygenase AurH (wildtype) from Streptomyces Thioluteus
ComponentsCytochrome P450
KeywordsOXIDOREDUCTASE / Cytochrome P450 / Monooxygenase
Function / homology
Function and homology information


cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic process / iron ion binding / heme binding
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
PROTOPORPHYRIN IX CONTAINING FE / Putative cytochrome P450
Similarity search - Component
Biological speciesStreptomyces thioluteus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsZocher, G. / Richter, M.E.A. / Mueller, U. / Hertweck, C.
CitationJournal: J.Am.Chem.Soc. / Year: 2011
Title: Structural fine-tuning of a multifunctional cytochrome p450 monooxygenase.
Authors: Zocher, G. / Richter, M.E. / Mueller, U. / Hertweck, C.
History
DepositionOct 5, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Feb 21, 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_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.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: Cytochrome P450
B: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,17910
Polymers90,1462
Non-polymers2,0338
Water6,071337
1
A: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1205
Polymers45,0731
Non-polymers1,0474
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0595
Polymers45,0731
Non-polymers9864
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)152.430, 54.140, 130.300
Angle α, β, γ (deg.)90.00, 123.32, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Cytochrome P450


Mass: 45073.086 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces thioluteus (bacteria) / Gene: aurH / Production host: Escherichia coli (E. coli) / References: UniProt: Q70KH6

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Non-polymers , 5 types, 345 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 337 / 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: 2.49 Å3/Da / Density % sol: 50.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M NaCl, 2.0M AS, 0.1 M Tris pH=8.6-8.8, 10 mg/mL , pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 5, 2008
RadiationMonochromator: DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.05→25 Å / Num. all: 56330 / Num. obs: 56058 / % possible obs: 99.5 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 3.8 % / Biso Wilson estimate: 25.4 Å2 / Rmerge(I) obs: 0.139 / Rsym value: 0.119 / Net I/σ(I): 9.1
Reflection shellResolution: 2.05→2.1 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.615 / Mean I/σ(I) obs: 2.7 / Num. unique all: 4164 / Rsym value: 0.499 / % possible all: 99.6

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.6.0085refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.874 / SU B: 11.783 / SU ML: 0.149 / Isotropic thermal model: TLS / Cross valid method: THROUGHOUT / ESU R Free: 0.208 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.26366 2606 5 %RANDOM
Rwork0.21448 ---
obs0.21693 49526 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 16.482 Å2
Baniso -1Baniso -2Baniso -3
1-3.29 Å2-0 Å21.62 Å2
2---1.09 Å20 Å2
3----0.42 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6300 0 132 337 6769
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0226612
X-RAY DIFFRACTIONr_bond_other_d0.0020.024418
X-RAY DIFFRACTIONr_angle_refined_deg0.7352.0059062
X-RAY DIFFRACTIONr_angle_other_deg0.688310718
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9615818
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.85323.377308
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.121151014
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.6951556
X-RAY DIFFRACTIONr_chiral_restr0.060.21000
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217433
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021355
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 188 -
Rwork0.24 3586 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.10670.0080.03860.33040.21150.20990.0290.0112-0.0158-0.0143-0.06990.0395-0.0572-0.0390.04090.07920.0122-0.00550.0595-0.00950.0315-3.20612.60337.6211
20.15140.0502-0.02660.2870.01830.21250.0086-0.0024-0.02160.0124-0.0252-0.019-0.0016-0.00470.01660.0072-0.0012-0.02050.06270.0040.0791-20.560634.9633-1.7313
30.0019-0.0005-0.00310.0004-0.0010.0186-0.0092-0.01970.0048-0.0006-0.0067-0.00530.02520.09510.01590.03560.13260.01750.49560.0760.0689-21.303129.78336.1182
40.0394-0.02530.04810.0659-0.0330.067-0.00140.0120.00960.0198-0.01940.01910.00120.0090.02080.0306-0.0092-0.01040.0764-0.00690.0787-11.349225.450815.7077
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 406
2X-RAY DIFFRACTION1A501
3X-RAY DIFFRACTION2B4 - 406
4X-RAY DIFFRACTION2B501
5X-RAY DIFFRACTION3A407 - 409
6X-RAY DIFFRACTION3B407 - 409
7X-RAY DIFFRACTION4A410
8X-RAY DIFFRACTION4B410 - 745

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