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- PDB-7ow9: Crystal structure of a staphylococcal orthologue of CYP134A1 (CYP... -

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Basic information

Entry
Database: PDB / ID: 7ow9
TitleCrystal structure of a staphylococcal orthologue of CYP134A1 (CYPX) in complex with Cyclo-L-leucyl-L-leucine
ComponentsCYPX
KeywordsBIOSYNTHETIC PROTEIN / CYP / Leucine / Cyclic / dipeptide / P450 / cyclodipeptide / pulcherrimin / Pulcherriminic / cypX / CYP134A1 / cyclo-L-leucyl-L-leucyl / Staphylococcus / aureus
Function / homologyChem-2IO / PROTOPORPHYRIN IX CONTAINING FE / NITRATE ION
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSnee, M. / Levy, C. / Leys, D. / Katariya, M. / Munro, A.W.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC) United Kingdom
CitationJournal: To Be Published
Title: Crystal structure of a staphylococcal orthologue of CYP134A1 (CYPX) in complex with Cyclo-L-leucyl-L-leucine
Authors: Snee, M. / Katariya, M.
History
DepositionJun 17, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 25, 2021Provider: repository / Type: Initial release
Revision 2.0Sep 29, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / diffrn_source / pdbx_data_processing_status / pdbx_poly_seq_scheme / pdbx_refine_tls_group / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_torsion / struct_conf / struct_conn / struct_ref_seq / struct_sheet_range
Item: _atom_site.auth_seq_id / _atom_site_anisotrop.pdbx_auth_seq_id ..._atom_site.auth_seq_id / _atom_site_anisotrop.pdbx_auth_seq_id / _diffrn_source.pdbx_synchrotron_site / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_refine_tls_group.beg_auth_seq_id / _pdbx_refine_tls_group.end_auth_seq_id / _pdbx_refine_tls_group.selection_details / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_residues.auth_seq_id / _pdbx_validate_torsion.auth_seq_id / _struct_conf.beg_auth_seq_id / _struct_conf.end_auth_seq_id / _struct_conn.ptnr1_auth_seq_id / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.end_auth_seq_id
Revision 2.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model
Item: _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CYPX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8794
Polymers45,9751
Non-polymers9053
Water5,278293
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-23 kcal/mol
Surface area17000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.179, 105.025, 104.219
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein CYPX


Mass: 45974.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: NCTC 5663 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41
#2: Chemical ChemComp-2IO / (3S,6S)-3,6-bis(2-methylpropyl)piperazine-2,5-dione / cyclo(L-Leu-L-Leu) / Leucinimid / 2,5-Piperazinedione, 3,6-bis(2-methylpropyl) / 137006


Mass: 226.315 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H22N2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#4: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 293 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.39 Å3/Da / Density % sol: 48.56 % / Description: Oblong and block-like
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M Ammonium Nitrate, 0.1M Bis Tris Propane pH 8.5, 18% V/V PEG smear High

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.8→54.37 Å / Num. obs: 40958 / % possible obs: 99.6 % / Redundancy: 13 % / Biso Wilson estimate: 30.75 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.0751 / Rpim(I) all: 0.021 / Rrim(I) all: 0.078 / Net I/σ(I): 18
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 13.2 % / Rmerge(I) obs: 1.047 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 1997 / CC1/2: 0.914 / Rpim(I) all: 0.295 / % possible all: 97.89

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
xia2data reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NC3

3nc3


Resolution: 1.8→52.11 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 22.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1996 2050 5.02 %
Rwork0.167 38803 -
obs0.1686 40853 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 156.37 Å2 / Biso mean: 46.4856 Å2 / Biso min: 22.96 Å2
Refinement stepCycle: final / Resolution: 1.8→52.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3170 0 115 293 3578
Biso mean--38.94 46.58 -
Num. residues----393
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.840.35571360.31362531266798
1.84-1.890.29751230.27542547267099
1.89-1.940.34341250.26322544266999
1.94-20.26111160.21832573268999
2-2.060.22791310.19892574270599
2.06-2.130.21681340.17612537267199
2.13-2.220.2251430.14792554269799
2.22-2.320.18191530.15572539269299
2.32-2.440.19661410.147526062747100
2.44-2.590.19291420.150225622704100
2.6-2.80.19051560.153825992755100
2.8-3.080.17011210.170126192740100
3.08-3.520.22351490.172226142763100
3.52-4.440.16541460.144326482794100
4.44-52.110.18771340.162227562890100
Refinement TLS params.Method: refined / Origin x: -16.957 Å / Origin y: -22.573 Å / Origin z: -5.749 Å
111213212223313233
T0.1954 Å2-0.0088 Å2-0.0043 Å2-0.2891 Å20.0125 Å2--0.2564 Å2
L0.8147 °20.1437 °20.5456 °2-0.4764 °20.2545 °2--2.3402 °2
S-0.0201 Å °0.0141 Å °0.054 Å °-0.0635 Å °-0.0121 Å °0.0227 Å °-0.1204 Å °0.0073 Å °0.0305 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 3:399 OR RESID 801:803 OR RESID 901:1193 ) )A3 - 399
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 3:399 OR RESID 801:803 OR RESID 901:1193 ) )A801 - 803
3X-RAY DIFFRACTION1( CHAIN A AND ( RESID 3:399 OR RESID 801:803 OR RESID 901:1193 ) )A901 - 1193

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