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- PDB-6q2u: Structure of Cytochrome C4 from Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 6q2u
TitleStructure of Cytochrome C4 from Pseudomonas aeruginosa
ComponentsCytochrome c4
KeywordsELECTRON TRANSPORT / Diheme / electron carrier
Function / homology
Function and homology information


periplasmic space / electron transfer activity / iron ion binding / heme binding
Similarity search - Function
Cytochrome c4-like / Cytochrome c / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
HEME C / C-type cytochrome / Cytochrome c4
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsCarpenter, J.M. / Zhong, F. / Pletneva, E.V. / Ragusa, M.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM113132 United States
CitationJournal: J.Inorg.Biochem. / Year: 2019
Title: Structure and redox properties of the diheme electron carrier cytochrome c4from Pseudomonas aeruginosa.
Authors: Carpenter, J.M. / Zhong, F. / Ragusa, M.J. / Louro, R.O. / Hogan, D.A. / Pletneva, E.V.
History
DepositionAug 8, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome c4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9333
Polymers18,6961
Non-polymers1,2372
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.408, 61.408, 173.262
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)

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Components

#1: Protein Cytochrome c4


Mass: 18696.100 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: cc4, cc4_1, cc4_2, ALP65_02559, C0044_40555, CAZ10_27455, CSB93_1138, DT376_12500, DY940_00700, DZ934_03190, DZ962_07080, ECC04_032935, EFK68_32500, EGV95_33620, EQH76_15100, IPC3_16700, IPC434_ ...Gene: cc4, cc4_1, cc4_2, ALP65_02559, C0044_40555, CAZ10_27455, CSB93_1138, DT376_12500, DY940_00700, DZ934_03190, DZ962_07080, ECC04_032935, EFK68_32500, EGV95_33620, EQH76_15100, IPC3_16700, IPC434_20475, IPC669_16455, PAERUG_E15_London_28_01_14_01385, PAMH19_3139, RW109_RW109_07107
Production host: Escherichia coli (E. coli) / References: UniProt: A0A071L1H9, UniProt: P00106*PLUS
#2: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.52 Å3/Da / Density % sol: 51.23 %
Crystal growTemperature: 296.15 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 0.2 M sodium chloride, 0.1 M sodium phosphate/citrate buffer pH 4.2, 18% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jan 31, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 1.85→39.12 Å / Num. obs: 17508 / % possible obs: 100 % / Redundancy: 18.1 % / Biso Wilson estimate: 32.28 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.149 / Rpim(I) all: 0.037 / Rrim(I) all: 0.154 / Net I/σ(I): 11.1 / Num. measured all: 316544 / Scaling rejects: 4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.85-1.89162.121641310290.7430.5392.1891.399.4
9.05-39.1213.20.09627762110.9970.0250.09924.898.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.53 Å39.12 Å
Translation4.53 Å39.12 Å

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
XDSdata reduction
Aimless0.7.4data scaling
PHASER2.8.2phasing
Cootmodel building
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1M70

1m70


Resolution: 1.85→39.12 Å / SU ML: 0.1786 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.4425
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2161 897 5.15 %
Rwork0.1785 16510 -
obs0.1806 17407 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.48 Å2
Refinement stepCycle: LAST / Resolution: 1.85→39.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1225 0 86 89 1400
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00571347
X-RAY DIFFRACTIONf_angle_d0.7511848
X-RAY DIFFRACTIONf_chiral_restr0.0417188
X-RAY DIFFRACTIONf_plane_restr0.0055234
X-RAY DIFFRACTIONf_dihedral_angle_d6.65661055
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.960.28321350.25652659X-RAY DIFFRACTION99.68
1.96-2.110.27091510.22332690X-RAY DIFFRACTION99.82
2.11-2.330.30321420.19672698X-RAY DIFFRACTION99.82
2.33-2.660.23971410.18742746X-RAY DIFFRACTION99.79
2.66-3.350.24741490.19162758X-RAY DIFFRACTION99.76
3.35-39.120.17591790.15392959X-RAY DIFFRACTION99.81
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)
10.336127704194-0.231054208244-0.05740536621440.259542373708-0.1611049367720.3999026705550.152879915419-0.09770968210770.04750155508740.1325012601270.01466158921360.01512561260210.0581788760115-0.0512717773381-8.65295745262E-50.299625439860.01976784949140.04164306143450.272475285827-0.01112473289250.28445924750313.937797181220.3686576043104.208163594
20.2113095272930.0676387045145-0.224644674520.0171427437426-0.06451300352370.2273338111740.0325355613048-0.1230552255140.490827557135-0.1181793189990.148989909455-0.229933379764-0.837379932226-0.1384928668350.00239391939210.5051265603740.04165908094260.1205049241450.22218992497-0.0005157672116050.42027652599912.563044224431.825132412597.6155986078
30.1903941477310.0276945399341-0.2709490303450.28424960295-0.3688694870970.6869518807950.169959097362-0.2413469570260.5788922223620.08840793825750.0204250002459-0.175977402697-0.24417124065-0.07219130910990.004753243685530.3410776746890.05211690176230.09666077669160.28714183317-0.04350884316430.39622945524310.765566147129.8225551351103.810092868
40.129315669249-0.00718358749122-0.1418689299940.0978781482874-0.04667607727030.1745069222280.213177507155-0.2338599031920.06023799587080.10940994873-0.09858883099190.07371335134260.316590521012-0.27904345452-5.52871243744E-60.383386212920.03542860439610.001620710877960.295761779803-0.01860954178030.3171283964815.75306773018.4871982298891.0537135506
50.0678211570771-0.0452174531844-0.008684651824620.0993394298544-0.02889525663770.01333112084990.1243536572690.194313875683-0.0298509642651-0.156859201699-0.194250443122-0.133858146424-0.340015740333-0.09561135847783.65471585246E-50.4270102647710.03197317405780.02912059835480.281858739771-0.01342903136330.28954915950116.445241722811.762976894177.9482943327
60.06341397767480.0849390864397-0.09641184048460.0986427829311-0.1150653573030.132718779165-0.07184291612730.4808113125110.407587229107-0.446331817625-0.03804499496860.0946122009593-0.687597700370.276407583867-0.008698941402640.4884080784380.02697440538290.03162244950580.4374871488960.07002120645520.30236103528916.099685610821.230938255775.0482695402
70.0498003413489-0.001007655423070.04956487525060.00380328558264-0.002071675614460.0615302123452-0.0280979508559-0.103741712083-0.0512900558711-0.1069151400140.2044310998890.03247288016440.2784028997710.01694338647421.96004525549E-50.2755385405680.02668069543590.04234503485190.221009062293-0.03371302963940.30162741128116.718956745418.264516894190.9102603557
80.04223525935070.004105577665590.01649632286010.1171299083060.006516401655020.07575067982950.1363321629020.1810373097-0.007639180914020.11802516451-0.116694057130.394527980624-0.219706029581-0.277785431771-0.001341869394710.3129750735860.1152442463930.02601196584820.3612789684620.02890060627520.3164678786344.754403033320.556909292386.4603770068
90.0761012308467-0.008884185490540.1854984016750.0102871455889-0.06382852546180.649417317355-0.3166930044180.1251685679320.436447831149-0.672163609842-0.0931220972695-0.000713587994727-0.912607051283-0.0708761944372-0.006854377327310.7912973906340.2378138426340.09693104961240.373079095510.151634283130.4667266668427.1581541177931.760454511485.3230564281
100.5230936056170.187804949174-0.4417431156670.198612510702-0.045583960010.4570619306090.07510780662710.1924043255140.137893627605-0.06060575969780.1332848154150.16056891779-0.320160061996-0.1601938738510.0005309807570960.4401942327920.08334779116040.04011138283470.2834815763440.03902816564370.31883873581310.55692507717.012116114981.5809585946
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 36 )
2X-RAY DIFFRACTION2chain 'A' and (resid 37 through 49 )
3X-RAY DIFFRACTION3chain 'A' and (resid 50 through 78 )
4X-RAY DIFFRACTION4chain 'A' and (resid 79 through 90 )
5X-RAY DIFFRACTION5chain 'A' and (resid 91 through 100 )
6X-RAY DIFFRACTION6chain 'A' and (resid 101 through 114 )
7X-RAY DIFFRACTION7chain 'A' and (resid 115 through 133 )
8X-RAY DIFFRACTION8chain 'A' and (resid 134 through 146 )
9X-RAY DIFFRACTION9chain 'A' and (resid 147 through 156 )
10X-RAY DIFFRACTION10chain 'A' and (resid 157 through 181 )

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