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- PDB-3ejb: Crystal Structure of P450BioI in complex with tetradecanoic acid ... -

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Basic information

Entry
Database: PDB / ID: 3ejb
TitleCrystal Structure of P450BioI in complex with tetradecanoic acid ligated Acyl Carrier Protein
Components
  • Acyl carrier protein
  • Biotin biosynthesis cytochrome P450-like enzyme
KeywordsOxidoreductase/Lipid Transport / Protein-Protein Complex / Cytochrome P450 Fold / Carrier Protein / 4-Helix Bundle / Fatty acid biosynthesis / Lipid synthesis / Phosphopantetheine / Biotin biosynthesis / Heme / Iron / Metal-binding / Monooxygenase / Oxidoreductase / Oxidoreductase-Lipid Transport COMPLEX
Function / homology
Function and homology information


pimeloyl-[acyl-carrier protein] synthase / biotin biosynthetic process / lipid biosynthetic process / lipid A biosynthetic process / acyl binding / acyl carrier activity / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / phosphopantetheine binding / monooxygenase activity / fatty acid biosynthetic process ...pimeloyl-[acyl-carrier protein] synthase / biotin biosynthetic process / lipid biosynthetic process / lipid A biosynthetic process / acyl binding / acyl carrier activity / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / phosphopantetheine binding / monooxygenase activity / fatty acid biosynthetic process / iron ion binding / response to xenobiotic stimulus / lipid binding / heme binding / membrane / cytosol / cytoplasm
Similarity search - Function
Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2 - #20 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2 / ACP-like / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Cytochrome P450, B-class / Acyl carrier protein (ACP) / Cytochrome p450 / Cytochrome P450 / Phosphopantetheine attachment site / Phosphopantetheine attachment site. ...Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2 - #20 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2 / ACP-like / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Cytochrome P450, B-class / Acyl carrier protein (ACP) / Cytochrome p450 / Cytochrome P450 / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Chem-ZMP / Acyl carrier protein / Biotin biosynthesis cytochrome P450
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Bacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 Å
AuthorsCryle, M.J. / Schlichting, I.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: Structural insights from a P450 Carrier Protein complex reveal how specificity is achieved in the P450(BioI) ACP complex.
Authors: Cryle, M.J. / Schlichting, I.
History
DepositionSep 18, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 24, 2016Group: Non-polymer description
Revision 1.3Jul 29, 2020Group: Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_entity_nonpoly / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acyl carrier protein
B: Biotin biosynthesis cytochrome P450-like enzyme
C: Acyl carrier protein
D: Biotin biosynthesis cytochrome P450-like enzyme
E: Acyl carrier protein
F: Biotin biosynthesis cytochrome P450-like enzyme
G: Acyl carrier protein
H: Biotin biosynthesis cytochrome P450-like enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)233,86326
Polymers226,6968
Non-polymers7,16718
Water24,1041338
1
A: Acyl carrier protein
B: Biotin biosynthesis cytochrome P450-like enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,4837
Polymers56,6742
Non-polymers1,8095
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4670 Å2
ΔGint-38 kcal/mol
Surface area20400 Å2
MethodPISA
2
C: Acyl carrier protein
D: Biotin biosynthesis cytochrome P450-like enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,4486
Polymers56,6742
Non-polymers1,7744
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4250 Å2
ΔGint-32 kcal/mol
Surface area20620 Å2
MethodPISA
3
E: Acyl carrier protein
F: Biotin biosynthesis cytochrome P450-like enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,4837
Polymers56,6742
Non-polymers1,8095
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4650 Å2
ΔGint-38 kcal/mol
Surface area20250 Å2
MethodPISA
4
G: Acyl carrier protein
H: Biotin biosynthesis cytochrome P450-like enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,4486
Polymers56,6742
Non-polymers1,7744
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4690 Å2
ΔGint-29 kcal/mol
Surface area20840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.300, 92.100, 107.700
Angle α, β, γ (deg.)109.00, 89.20, 90.10
Int Tables number1
Space group name H-MP1
Detailsheterodimers are formed by chain A and B, C and D, E and F, G and H.

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Components

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Protein , 2 types, 8 molecules ACEGBDFH

#1: Protein
Acyl carrier protein / ACP / Cytosolic-activating factor / CAF / Fatty acid synthase acyl carrier protein


Mass: 10685.630 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: acpP, b1094, JW1080 / Plasmid: pET28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: P0A6A8
#2: Protein
Biotin biosynthesis cytochrome P450-like enzyme


Mass: 45988.352 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: GP208 / Gene: bioI, CYP107H, BSU30190 / Plasmid: pET24b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P53554, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen

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Sugars , 1 types, 8 molecules

#4: Sugar
ChemComp-HTG / heptyl 1-thio-beta-D-glucopyranoside / HEPTYL 1-THIOHEXOPYRANOSIDE / heptyl 1-thio-beta-D-glucoside / heptyl 1-thio-D-glucoside / heptyl 1-thio-glucoside


Type: D-saccharide / Mass: 294.408 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C13H26O5S / Comment: detergent*YM

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Non-polymers , 4 types, 1348 molecules

#3: Chemical
ChemComp-ZMP / S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] tetradecanethioate


Mass: 568.704 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C25H49N2O8PS
#5: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1338 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.54 Å3/Da / Density % sol: 51.49 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M Na HEPES, 0.25 M NaCl, 0.15 M Li2SO4, 19% PEG 4000, 0.2% n-heptyl b-D-thioglucopyranoside, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.98089 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 8, 2008
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98089 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 149113 / Num. obs: 144447 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.9 % / Biso Wilson estimate: 25.9 Å2 / Rsym value: 0.0604 / Net I/σ(I): 21.8
Reflection shellResolution: 2→2.05 Å / Redundancy: 7.4 % / Mean I/σ(I) obs: 7.4 / Rsym value: 0.33 / % possible all: 94.9

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Processing

Software
NameVersionClassification
XDSdata scaling
Cootmodel building
REFMAC5.2.0005refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: SAD Structure

Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.904 / SU B: 4.965 / SU ML: 0.141 / Cross valid method: THROUGHOUT / ESU R: 0.215 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.266 7336 5 %RANDOM
Rwork0.222 ---
obs0.224 139586 97.7 %-
all-149113 --
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: 28.83 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å2-0.06 Å20.16 Å2
2--0.83 Å21.97 Å2
3---0.88 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14661 0 401 1338 16400
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.02215405
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.4992.01520896
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9251835
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.5224.477717
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.715152662
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3411599
X-RAY DIFFRACTIONr_chiral_restr0.0360.22335
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0211519
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1890.37541
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3140.510717
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.51811
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.150.3108
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1750.565
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3511.59487
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.615214954
X-RAY DIFFRACTIONr_scbond_it0.61336577
X-RAY DIFFRACTIONr_scangle_it0.9834.55932
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% reflection
Rfree0.293 544 -
Rwork0.257 10218 -
obs--96.72 %

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