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- PDB-3nc5: CYP134A1 structure with an open substrate binding loop -

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Basic information

Entry
Database: PDB / ID: 3nc5
TitleCYP134A1 structure with an open substrate binding loop
ComponentsCytochrome P450 cypX
KeywordsOXIDOREDUCTASE / Cytochrome P450 Oxidase / Haem Protein
Function / homology
Function and homology information


pulcherriminic acid synthase / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced iron-sulfur protein as one donor, and incorporation of one atom of oxygen / pigment biosynthetic process / iron ion binding / heme binding
Similarity search - Function
Cytochrome P450, CypX / 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 / Pulcherriminic acid synthase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å
AuthorsCryle, M.J. / Schlichting, I.
CitationJournal: Biochemistry / Year: 2010
Title: Structural and biochemical characterization of the cytochrome P450 CypX (CYP134A1) from Bacillus subtilis: a cyclo-L-leucyl-L-leucyl dipeptide oxidase.
Authors: Cryle, M.J. / Bell, S.G. / Schlichting, I.
History
DepositionJun 4, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 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.ptnr2_auth_asym_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_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 cypX
B: Cytochrome P450 cypX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,2629
Polymers98,7722
Non-polymers1,4907
Water57632
1
A: Cytochrome P450 cypX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1435
Polymers49,3861
Non-polymers7574
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cytochrome P450 cypX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1194
Polymers49,3861
Non-polymers7333
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.800, 105.400, 143.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115A6 - 61
2115B6 - 61
1125A90 - 403
2125B90 - 403
1134A1 - 406
2134B1 - 406

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Cytochrome P450 cypX


Mass: 49386.129 Da / Num. of mol.: 2 / Mutation: A356T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: BSU35060, cyp134, cypB, cypX / Plasmid: pET28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3
References: UniProt: O34926, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen
#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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 2.66 Å3/Da / Density % sol: 53.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M Bis-Tris, 0.1 M MgCl2, 12% (w/v) polyethylene glycol-3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 30, 2009
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→40.62 Å / Num. obs: 21929 / % possible obs: 95.8 % / Observed criterion σ(I): 3 / Redundancy: 3.9 % / Biso Wilson estimate: 68.5 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 9.1
Reflection shellResolution: 2.9→2.975 Å / Redundancy: 4 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 4.1 / Num. unique all: 1901 / % possible all: 90.3

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Processing

Software
NameVersionClassification
XDSdata scaling
SHARPphasing
REFMAC5.5.0070refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.9→40.62 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.858 / SU B: 39.311 / SU ML: 0.393 / Cross valid method: THROUGHOUT / ESU R Free: 0.491 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30637 1091 5 %RANDOM
Rwork0.23093 ---
obs0.23468 21929 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.319 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.9→40.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6003 0 101 32 6136
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0226233
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2542.0128468
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0935751
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.63424.075292
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.186151067
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5251544
X-RAY DIFFRACTIONr_chiral_restr0.0870.2940
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214722
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2761.53784
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.53626123
X-RAY DIFFRACTIONr_scbond_it0.87832449
X-RAY DIFFRACTIONr_scangle_it1.4794.52345
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
1224MEDIUM POSITIONAL0.230.5
1264LOOSE POSITIONAL0.385
1224MEDIUM THERMAL0.262
1264LOOSE THERMAL0.2810
21240MEDIUM POSITIONAL0.270.5
21173LOOSE POSITIONAL0.595
21240MEDIUM THERMAL1.112
21173LOOSE THERMAL1.3710
343MEDIUM POSITIONAL0.150.5
343MEDIUM THERMAL0.642
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.404 78 -
Rwork0.291 1497 -
obs-1497 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)
113.19611.0953-0.27458.0833-6.580914.6244-0.10370.4940.3235-0.22170.08770.80360.1879-0.85590.0160.2235-0.00310.00970.85620.01490.7747.1752-3.3903-11.1383
26.86920.5141-1.19222.27041.08012.7887-0.01960.5255-0.38860.112-0.18030.55150.5547-0.3540.19990.4131-0.01010.05210.70680.03890.219321.863-17.2719-9.3896
35.4453-1.68731.085113.08083.2395.46020.10970.43570.4981-0.8590.1772-0.3272-0.38740.1428-0.28690.30340.07070.09230.49580.11220.247145.2793-9.8815-21.9719
42.1509-0.6223-0.28022.13682.30084.6660.05190.1288-0.34890.02630.0030.06040.4359-0.0279-0.05490.28610.04550.05480.52040.11510.112633.3419-17.7076-17.0733
55.2634-0.1292-0.80624.24741.2454.98490.1654-0.02820.06560.3524-0.09660.17010.2217-0.269-0.06880.22870.0720.09090.51020.05470.04330.4956-8.6009-5.6263
620.31852.0822-18.75629.76972.186626.23590.2413-0.67890.0660.0118-0.6054-0.40090.72270.64610.36410.4053-0.05820.02081.164-0.04190.919657.124919.925523.0175
76.6336-1.3063-3.10481.41090.7443.31770.0186-0.60610.09580.04720.2257-0.49160.05510.783-0.24430.3675-0.0201-0.00320.7835-0.07460.283940.12927.875820.5786
85.3441.51972.49611.6495-1.29774.5610.1049-0.09440.24930.3712-0.02770.1293-0.42790.0978-0.07720.34160.0414-0.0450.6437-0.15190.118227.426910.833536.9149
93.77410.5342-1.15431.3856-0.15154.71940.13880.097-0.1013-0.38930.0463-0.3416-0.00570.4499-0.18510.31240.00440.02460.5259-0.16320.227133.35877.920419.9016
105.3431-0.5033-0.63344.1782.06823.50340.3239-0.39540.7049-0.36270.1148-0.1271-0.74870.2369-0.43870.4008-0.04080.04860.5129-0.01580.168327.17417.044920.439
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 10
2X-RAY DIFFRACTION2A11 - 109
3X-RAY DIFFRACTION3A110 - 154
4X-RAY DIFFRACTION4A155 - 290
5X-RAY DIFFRACTION5A291 - 403
6X-RAY DIFFRACTION6B6 - 10
7X-RAY DIFFRACTION7B11 - 116
8X-RAY DIFFRACTION8B117 - 186
9X-RAY DIFFRACTION9B187 - 336
10X-RAY DIFFRACTION10B337 - 403

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