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- PDB-2hl7: Crystal structure of the periplasmic domain of CcmH from Pseudomo... -

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Basic information

Entry
Database: PDB / ID: 2hl7
TitleCrystal structure of the periplasmic domain of CcmH from Pseudomonas aeruginosa
ComponentsCytochrome C-type biogenesis protein CcmH
KeywordsOXIDOREDUCTASE / Three-helices bundle
Function / homology
Function and homology information


cytochrome complex assembly / metal ion binding / plasma membrane
Similarity search - Function
Cytochrome C biogenesis protein / CcmH/CycL/Ccl2/NrfF family / CcmH/CycL/Ccl2/NrfF domain superfamily / Cytochrome C biogenesis protein / : / Helicase, Ruva Protein; domain 3 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Cytochrome c-type biogenesis protein CcmH
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD, MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsDi Matteo, A. / Travaglini-Allocatelli, C. / Gianni, S. / Brunori, M.
Citation
Journal: J.Biol.Chem. / Year: 2007
Title: A strategic protein in cytochrome c maturation: three-dimensional structure of CcmH and binding to apocytochrome c
Authors: Di Matteo, A. / Gianni, S. / Schinina, M.E. / Giorgi, A. / Altieri, F. / Calosci, N. / Brunori, M. / Travaglini-Allocatelli, C.
#1: Journal: Arch.Microbiol. / Year: 1999
Title: Characterization of the Escherichia coli CcmH protein reveals new insights into the redox pathway required for cytochrome c maturation
Authors: Fabianek, R.A. / Hofer, T. / Thony-Meyer, L.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 2005
Title: AtCCMH, an essential component of the c-type cytochrome maturation pathway in Arabidopsis mitochondria, interacts with apocytochrome c
Authors: Meyer, E.H. / Giege, P. / Gelhaye, E. / Rayapuram, N. / Ahuja, U. / Thony-Meyer, L. / Grienenberger, J.M. / Bonnard, G.
History
DepositionJul 6, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 10, 2007Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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
Remark 999SEQUENCE This coordinates is used non-sequential residue numbering. Number 0 was simply skipped in ...SEQUENCE This coordinates is used non-sequential residue numbering. Number 0 was simply skipped in the numbering and have nothing to do with lack of electron density.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytochrome C-type biogenesis protein CcmH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,0153
Polymers9,6271
Non-polymers3882
Water1,26170
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.073, 45.414, 48.127
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-type biogenesis protein CcmH / Thiolo:disulfide interchange protein CCMH / CcmH: Thiol-oxidoreductase


Mass: 9626.693 Da / Num. of mol.: 1 / Fragment: Periplasmic domain, residues 1-80
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Plasmid: pET28 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q9I3N0
#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.2745.9
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2941vapor diffusion, hanging drop8.520% PEG 1000, 0.1M Tris-HCl , pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
2942vapor diffusion, hanging drop838% PEG 6000, 0.8M NaCl, 0.1M Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID2910.97920, 0.97940, 0.97560
SYNCHROTRONESRF ID14-420.931
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDFeb 15, 2005
MAR CCD 165 mm2CCDJul 15, 2005
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-IDMonochromator
1MADMx-ray1
2SINGLE WAVELENGTHMx-ray1Khozu monochromator with a McLennon controller containing a LN2 cooled Si111 crystal
Radiation wavelength
IDWavelength (Å)Relative weight
10.97921
20.97941
30.97561
40.9311
ReflectionResolution: 1.7→33 Å / Num. all: 10212 / Num. obs: 10212 / % possible obs: 97.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 1.7→1.76 Å / % possible all: 96.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD, MOLECULAR REPLACEMENT / Resolution: 1.7→30 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.757 / SU ML: 0.09 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.125 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23493 478 4.8 %RANDOM
Rwork0.20941 ---
all0.21065 10116 --
obs0.21065 9417 97.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 32.849 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å20 Å2
2---1.21 Å20 Å2
3---1.37 Å2
Refinement stepCycle: LAST / Resolution: 1.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms653 0 20 70 743
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.022684
X-RAY DIFFRACTIONr_angle_refined_deg1.3581.972914
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.276581
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.00224.47438
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.12215113
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.972156
X-RAY DIFFRACTIONr_chiral_restr0.10.291
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02529
X-RAY DIFFRACTIONr_nbd_refined0.2160.2343
X-RAY DIFFRACTIONr_nbtor_refined0.3120.2460
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2090.256
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2470.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1040.217
X-RAY DIFFRACTIONr_mcbond_it1.0161.5419
X-RAY DIFFRACTIONr_mcangle_it1.6212651
X-RAY DIFFRACTIONr_scbond_it2.3113298
X-RAY DIFFRACTIONr_scangle_it3.3544.5263
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 31 -
Rwork0.281 675 -
obs--95.41 %
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)
15.8401-1.74350.82028.8753-1.46763.9838-0.00810.2071-0.0958-0.53890.01130.01390.2476-0.0993-0.00320.01980.00210.0161-0.04240.0099-0.0953-0.53416.12911.271
25.8195-5.0253.20058.9002-7.19236.0603-0.1506-0.1930.22410.780.028-0.4328-0.61260.00390.12260.0770.0062-0.0779-0.0435-0.0434-0.05294.30820.14520.715
35.8556-5.86722.311417.6465-3.88149.0928-0.3787-0.26090.64810.50570.2742-2.5232-0.79770.30980.1045-0.1029-0.0245-0.0405-0.053-0.05430.397810.94424.82514.843
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA13 - 2617 - 30
2X-RAY DIFFRACTION2AA42 - 5946 - 63
3X-RAY DIFFRACTION3AA61 - 7465 - 78

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