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- PDB-3tyw: Crystal Structure of CYP105N1 from Streptomyces coelicolor A3(2) -

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Basic information

Entry
Database: PDB / ID: 3tyw
TitleCrystal Structure of CYP105N1 from Streptomyces coelicolor A3(2)
ComponentsPutative cytochrome P450
KeywordsOXIDOREDUCTASE / P450 monooxygenase
Function / homology
Function and homology information


oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / 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 / Cytochrome P450
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsZhao, B. / Waterman, M.R.
CitationJournal: To be Published
Title: Crystal Structure of CYP105N1 from Streptomyces coelicolor A3(2)
Authors: Zhao, B. / Waterman, M.R.
History
DepositionSep 26, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 11, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Feb 28, 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_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_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

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Assembly

Deposited unit
A: Putative cytochrome P450
B: Putative cytochrome P450
C: Putative cytochrome P450
D: Putative cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)186,4068
Polymers183,9404
Non-polymers2,4664
Water1,71195
1
A: Putative cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6012
Polymers45,9851
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6012
Polymers45,9851
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Putative cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6012
Polymers45,9851
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Putative cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6012
Polymers45,9851
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Putative cytochrome P450
hetero molecules

D: Putative cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,2034
Polymers91,9702
Non-polymers1,2332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z+1/31
Buried area2130 Å2
ΔGint-12 kcal/mol
Surface area34200 Å2
MethodPISA
6
B: Putative cytochrome P450
hetero molecules

C: Putative cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,2034
Polymers91,9702
Non-polymers1,2332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_444-x+y-1,-x-1,z-1/31
Buried area2230 Å2
ΔGint-13 kcal/mol
Surface area34260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.537, 134.537, 230.580
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein
Putative cytochrome P450


Mass: 45984.949 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Gene: SCO7686 / Plasmid: pET17b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21pylus / References: UniProt: Q9EWP1
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 3.27 Å3/Da / Density % sol: 62.44 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 3350, HEPES 7.0, Sodium Formate, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jan 27, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.9→40 Å / Num. all: 51850 / Num. obs: 51760 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.091 / Rsym value: 0.071 / Net I/σ(I): 26.8
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 9.9 % / Rmerge(I) obs: 0.139 / Mean I/σ(I) obs: 6.1 / Rsym value: 0.542 / % possible all: 99.8

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Processing

Software
NameClassification
HKL-2000data collection
PHASERphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→30 Å / Isotropic thermal model: Isotropic / σ(F): 0.2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.3005 2590 -RANDOM
Rwork0.2821 ---
all0.2842 51872 --
obs0.2821 51695 99.7 %-
Displacement parametersBiso mean: 65.21 Å2
Baniso -1Baniso -2Baniso -3
1--1.09 Å2-1.09 Å22.18 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.54 Å0.5 Å
Luzzati d res low-5 Å
Luzzati sigma a0.93 Å0.89 Å
Refinement stepCycle: LAST / Resolution: 2.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12366 0 172 95 12633
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
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_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.9→3.04 Å / Rfactor Rfree error: 0.025
RfactorNum. reflection% reflection
Rfree0.454 320 -
Rwork0.431 --
obs--5 %

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