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- PDB-3ejd: Crystal Structure of P450BioI in complex with hexadec-9Z-enoic ac... -

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Basic information

Entry
Database: PDB / ID: 3ejd
TitleCrystal Structure of P450BioI in complex with hexadec-9Z-enoic 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 / cholest-4-en-3-one 26-monooxygenase activity / lipid A biosynthetic process / lipid biosynthetic process / steroid hydroxylase activity / phosphopantetheine binding / cholesterol catabolic process / acyl binding / acyl carrier activity ...pimeloyl-[acyl-carrier protein] synthase / biotin biosynthetic process / cholest-4-en-3-one 26-monooxygenase activity / lipid A biosynthetic process / lipid biosynthetic process / steroid hydroxylase activity / phosphopantetheine binding / cholesterol catabolic process / acyl binding / acyl carrier activity / fatty acid biosynthetic process / response to xenobiotic stimulus / iron ion binding / lipid binding / heme binding / cytosol / cytoplasm
Similarity search - Function
Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2 - #20 / ACP-like / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2 / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Acyl carrier protein (ACP) / Cytochrome P450, B-class / Cytochrome p450 / Cytochrome P450 / Phosphopantetheine attachment site / Phosphopantetheine attachment site. ...Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2 - #20 / ACP-like / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2 / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Acyl carrier protein (ACP) / Cytochrome P450, B-class / Cytochrome p450 / Cytochrome P450 / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Phosphopantetheine attachment site / ACP-like superfamily / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / 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-ZMQ / 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: 2.1 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 1.2Mar 8, 2017Group: 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_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.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)233,96726
Polymers226,6968
Non-polymers7,27118
Water18,1951010
1
A: Acyl carrier protein
B: Biotin biosynthesis cytochrome P450-like enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5097
Polymers56,6742
Non-polymers1,8355
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4410 Å2
ΔGint-40 kcal/mol
Surface area20770 Å2
MethodPISA
2
C: Acyl carrier protein
D: Biotin biosynthesis cytochrome P450-like enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,4746
Polymers56,6742
Non-polymers1,8004
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4270 Å2
ΔGint-35 kcal/mol
Surface area20790 Å2
MethodPISA
3
E: Acyl carrier protein
F: Biotin biosynthesis cytochrome P450-like enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5097
Polymers56,6742
Non-polymers1,8355
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4580 Å2
ΔGint-40 kcal/mol
Surface area20220 Å2
MethodPISA
4
G: Acyl carrier protein
H: Biotin biosynthesis cytochrome P450-like enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,4746
Polymers56,6742
Non-polymers1,8004
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4250 Å2
ΔGint-33 kcal/mol
Surface area20490 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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
31E
41G
12B
22D
32F
42H

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112A19 - 94
2112C19 - 94
3112E19 - 94
4112G19 - 94
1122B10 - 394
2122D10 - 394
3122F10 - 394
4122H10 - 394

NCS ensembles :
ID
1
2
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


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, 1020 molecules

#3: Chemical
ChemComp-ZMQ / S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] (9Z)-hexadec-9-enethioate


Mass: 594.741 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H51N2O8PS
#5: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


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


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


Mass: 18.015 Da / Num. of mol.: 1010 / 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: 2.54 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: 2.1→50 Å / Num. obs: 119441 / % possible obs: 91.1 % / Redundancy: 2.6 % / Biso Wilson estimate: 31 Å2 / Rsym value: 0.086 / Net I/σ(I): 10.1
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 3.2 / Num. unique all: 16965 / % possible all: 82.7

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Processing

Software
NameVersionClassification
XDSdata scaling
Cootmodel building
REFMAC5.2.0005refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.898 / SU B: 7.612 / SU ML: 0.197 / Cross valid method: THROUGHOUT / ESU R: 0.281 / ESU R Free: 0.226 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28532 6319 5 %RANDOM
Rwork0.24088 ---
obs0.24311 119441 96.84 %-
all-313033 --
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: 34.278 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å20.05 Å2-0.02 Å2
2--0.61 Å22.6 Å2
3---1.33 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14645 0 402 1010 16057
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.02215354
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.6622.01520818
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.02151824
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.21824.482714
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.866152646
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9711598
X-RAY DIFFRACTIONr_chiral_restr0.0490.22329
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0211478
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1890.27417
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.210640
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.2965
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2020.2129
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1210.221
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5091.59439
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.896214900
X-RAY DIFFRACTIONr_scbond_it0.74836559
X-RAY DIFFRACTIONr_scangle_it1.24.55910
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A304tight positional0.020.05
12C304tight positional0.020.05
13E304tight positional0.020.05
14G304tight positional0.020.05
21B1512tight positional0.030.05
22D1512tight positional0.030.05
23F1512tight positional0.020.05
24H1512tight positional0.030.05
11A288medium positional0.480.5
12C288medium positional0.530.5
13E288medium positional0.530.5
14G288medium positional0.560.5
21B1513medium positional0.570.5
22D1513medium positional0.530.5
23F1513medium positional0.530.5
24H1513medium positional0.540.5
11A304tight thermal0.030.5
12C304tight thermal0.030.5
13E304tight thermal0.030.5
14G304tight thermal0.030.5
21B1512tight thermal0.040.5
22D1512tight thermal0.030.5
23F1512tight thermal0.030.5
24H1512tight thermal0.050.5
11A288medium thermal0.222
12C288medium thermal0.242
13E288medium thermal0.222
14G288medium thermal0.232
21B1513medium thermal0.262
22D1513medium thermal0.242
23F1513medium thermal0.252
24H1513medium thermal0.32
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 435 -
Rwork0.326 8723 -
obs-8723 96.33 %

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