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- PDB-4jmb: Crystal structure of Cytochrome C Peroxidase W191G-Gateless in co... -

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Basic information

Entry
Database: PDB / ID: 4jmb
TitleCrystal structure of Cytochrome C Peroxidase W191G-Gateless in complex with 5,6,7,8-tetrahydrothieno[2,3-b]quinolin-4-amine
ComponentsCytochrome c peroxidase
KeywordsOXIDOREDUCTASE / Model system / bulk solvent / ordered waters / docking / ligand binding
Function / homology
Function and homology information


cytochrome-c peroxidase activity / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / cellular response to oxidative stress / mitochondrial matrix / heme binding / membrane / metal ion binding
Similarity search - Function
Class I peroxidase / Heme-binding peroxidase Ccp1-like / Peroxidase; domain 2 / Peroxidase, domain 2 / Peroxidase; domain 1 - #10 / Peroxidase; domain 1 / Peroxidases heam-ligand binding site / Peroxidase, active site / Peroxidases active site signature. / Plant heme peroxidase family profile. ...Class I peroxidase / Heme-binding peroxidase Ccp1-like / Peroxidase; domain 2 / Peroxidase, domain 2 / Peroxidase; domain 1 - #10 / Peroxidase; domain 1 / Peroxidases heam-ligand binding site / Peroxidase, active site / Peroxidases active site signature. / Plant heme peroxidase family profile. / Haem peroxidase / Peroxidase / Peroxidases proximal heme-ligand signature. / Haem peroxidase superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
5,6,7,8-tetrahydrothieno[2,3-b]quinolin-4-amine / PROTOPORPHYRIN IX CONTAINING FE / Peroxidase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsBarelier, S. / Fischer, M.
CitationJournal: To be published
Title: Docking to a water-filled model binding site in Cytochrome c Peroxidase
Authors: Barelier, S. / Boyce, S.E. / Fish, I. / Fischer, M. / Goodin, D.B. / Shoichet, B.K.
History
DepositionMar 13, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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: Cytochrome c peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9454
Polymers32,9291
Non-polymers1,0163
Water6,954386
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)106.820, 74.800, 50.970
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cytochrome c peroxidase


Mass: 32928.582 Da / Num. of mol.: 1 / Fragment: RESIDUES 72-362, DELETIONS G192-A193 / Mutation: P190G, W191G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: RM11-1a / Gene: CCP1 CCP CPO YKR066C, SCRG_04081 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B3LRE1, cytochrome-c peroxidase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-1LW / 5,6,7,8-tetrahydrothieno[2,3-b]quinolin-4-amine


Mass: 204.291 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H12N2S
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 386 / 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: 3.09 Å3/Da / Density % sol: 60.22 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 6
Details: Apo crystal grown in 500mM MES, pH 6.0. Soaked into 100mM ZINC00346401 in 500mM MES, pH 6.0, 25% MPD (30min), vapor diffusion, sitting drop, temperature 283K

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.115869 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 8, 2011
RadiationMonochromator: Double flat crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.115869 Å / Relative weight: 1
ReflectionResolution: 1.2→50 Å / Num. obs: 100525 / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassificationNB
PHENIX1.6_289refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→29.19 Å / Occupancy max: 1 / Occupancy min: 0.2 / SU ML: 0.14 / σ(F): 1.99 / Phase error: 16.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1756 5047 5.02 %
Rwork0.166 --
obs0.1665 100520 99.51 %
all-105567 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.144 Å2 / ksol: 0.384 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.1975 Å20 Å20 Å2
2--2.9665 Å2-0 Å2
3---0.231 Å2
Refinement stepCycle: LAST / Resolution: 1.3→29.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2328 0 69 386 2783
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052629
X-RAY DIFFRACTIONf_angle_d0.9923591
X-RAY DIFFRACTIONf_dihedral_angle_d16.925967
X-RAY DIFFRACTIONf_chiral_restr0.07345
X-RAY DIFFRACTIONf_plane_restr0.005479
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.31480.241670.2273174X-RAY DIFFRACTION100
1.3148-1.33020.22131680.22043180X-RAY DIFFRACTION100
1.3302-1.34650.23011650.20383134X-RAY DIFFRACTION100
1.3465-1.36350.23511660.20143152X-RAY DIFFRACTION100
1.3635-1.38150.19221660.20013157X-RAY DIFFRACTION100
1.3815-1.40040.19331650.19463140X-RAY DIFFRACTION100
1.4004-1.42040.22821670.19553174X-RAY DIFFRACTION100
1.4204-1.44160.19741670.19323169X-RAY DIFFRACTION100
1.4416-1.46410.17361670.17723181X-RAY DIFFRACTION100
1.4641-1.48810.18881670.17853159X-RAY DIFFRACTION100
1.4881-1.51380.18571650.17023150X-RAY DIFFRACTION100
1.5138-1.54130.17621680.16693187X-RAY DIFFRACTION100
1.5413-1.57090.18071680.16853195X-RAY DIFFRACTION100
1.5709-1.6030.16881660.16533144X-RAY DIFFRACTION100
1.603-1.63790.18771480.15893216X-RAY DIFFRACTION100
1.6379-1.67590.16411480.16313180X-RAY DIFFRACTION100
1.6759-1.71790.14671770.15763196X-RAY DIFFRACTION100
1.7179-1.76430.17151450.16093189X-RAY DIFFRACTION100
1.7643-1.81620.16551810.16163196X-RAY DIFFRACTION100
1.8162-1.87480.1711820.16543152X-RAY DIFFRACTION100
1.8748-1.94180.18371790.16433195X-RAY DIFFRACTION100
1.9418-2.01950.15121640.15893199X-RAY DIFFRACTION100
2.0195-2.11140.15511670.1553200X-RAY DIFFRACTION100
2.1114-2.22270.17411850.15383192X-RAY DIFFRACTION100
2.2227-2.36190.16411810.15533187X-RAY DIFFRACTION100
2.3619-2.54420.17541820.16043222X-RAY DIFFRACTION100
2.5442-2.80.14971750.15953215X-RAY DIFFRACTION100
2.8-3.20480.15961500.16053278X-RAY DIFFRACTION100
3.2048-4.0360.18581920.14613237X-RAY DIFFRACTION99
4.036-29.19690.16651590.16323123X-RAY DIFFRACTION90

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