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- PDB-4pwa: Crystal structure of the c-type cytochrome SorU from Sinorhizobiu... -

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Basic information

Entry
Database: PDB / ID: 4pwa
TitleCrystal structure of the c-type cytochrome SorU from Sinorhizobium meliloti
ComponentsPutative cytochrome C
KeywordsELECTRON TRANSPORT / C-TYPE CYTOCHROME / HEME / ELECTRON TRANSFER
Function / homology
Function and homology information


electron transfer activity / heme binding / metal ion binding
Similarity search - Function
Cytochrome C oxidase, cbb3-type, subunit III / 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 / Cytochrome C
Similarity search - Component
Biological speciesSinorhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsLaming, E.M. / McGrath, A.P. / Maher, M.J.
CitationJournal: Elife / Year: 2015
Title: Structural basis of interprotein electron transfer in bacterial sulfite oxidation.
Authors: McGrath, A.P. / Laming, E.L. / Casas Garcia, G.P. / Kvansakul, M. / Guss, J.M. / Trewhella, J. / Calmes, B. / Bernhardt, P.V. / Hanson, G.R. / Kappler, U. / Maher, M.J.
History
DepositionMar 19, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2016Group: Database references
Revision 1.2Feb 15, 2017Group: Database references
Revision 1.3Sep 20, 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 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _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_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 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: Putative cytochrome C
B: Putative cytochrome C
C: Putative cytochrome C
D: Putative cytochrome C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0898
Polymers45,6154
Non-polymers2,4744
Water4,089227
1
A: Putative cytochrome C
C: Putative cytochrome C
hetero molecules

A: Putative cytochrome C
C: Putative cytochrome C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0898
Polymers45,6154
Non-polymers2,4744
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area8530 Å2
ΔGint-119 kcal/mol
Surface area15760 Å2
MethodPISA
2
B: Putative cytochrome C
D: Putative cytochrome C
hetero molecules

B: Putative cytochrome C
D: Putative cytochrome C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0898
Polymers45,6154
Non-polymers2,4744
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation14_555-x+1/2,-y+1/2,z1
Buried area8810 Å2
ΔGint-118 kcal/mol
Surface area15810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.949, 129.327, 197.059
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11C
21B
31A
41D

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Components

#1: Protein
Putative cytochrome C


Mass: 11403.683 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 28-113
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Strain: 1021 / Gene: R02831, SMc04048 / Plasmid: PET-SMC04048TAG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q92M25
#2: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / 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

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Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.35 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 1.8M TRI-SODIUM CITRATE PH 5.5, 0.1M GLYCINE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 / Wavelength: 0.954 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 1, 2011
RadiationMonochromator: SI VORTEX ES / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.19→50 Å / Num. obs: 23434 / % possible obs: 99.9 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.133 / Net I/σ(I): 6
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.796 / Mean I/σ(I) obs: 1.6 / % possible all: 100

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 4PW9

4pw9


Resolution: 2.19→39.19 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.925 / SU B: 10.012 / SU ML: 0.151 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.22 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.241 1201 5.2 %RANDOM
Rwork0.185 ---
obs0.188 23314 98.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.84 Å2
Baniso -1Baniso -2Baniso -3
1-4.09 Å20 Å20 Å2
2---1.64 Å20 Å2
3----2.45 Å2
Refinement stepCycle: LAST / Resolution: 2.19→39.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2528 0 172 227 2927
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222780
X-RAY DIFFRACTIONr_bond_other_d0.0010.021724
X-RAY DIFFRACTIONr_angle_refined_deg1.2422.1863831
X-RAY DIFFRACTIONr_angle_other_deg0.883.0044263
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7395344
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.6626.814113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.12915428
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.7951512
X-RAY DIFFRACTIONr_chiral_restr0.0580.2422
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213138
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02430
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4491.51718
X-RAY DIFFRACTIONr_mcbond_other0.0991.5690
X-RAY DIFFRACTIONr_mcangle_it0.87422750
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.4631062
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.4064.51079
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1C477medium positional0.340.5
2B477medium positional0.150.5
3A477medium positional0.180.5
4D477medium positional0.340.5
1C449loose positional0.575
2B449loose positional0.435
3A449loose positional0.495
4D449loose positional0.525
1C477medium thermal0.332
2B477medium thermal0.42
3A477medium thermal0.332
4D477medium thermal0.342
1C449loose thermal0.3610
2B449loose thermal0.4210
3A449loose thermal0.4710
4D449loose thermal0.4310
LS refinement shellResolution: 2.19→2.24 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 80 -
Rwork0.314 1431 -
obs--88.05 %
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)
12.2658-1.10940.26962.8184-1.18763.74110.0749-0.1467-0.3082-0.11520.02010.17560.1169-0.2358-0.0950.1225-0.0619-0.04760.07630.0360.0542-9.471348.926813.7077
22.86990.53710.77043.6101-0.98275.44390.00220.09450.0198-0.19680.05510.19420.3168-0.1927-0.05720.0832-0.0134-0.01750.04940.02370.023-0.574337.283735.9155
33.95591.19560.9644.6084-0.08185.27820.3005-0.1986-0.37230.1277-0.2048-0.25810.36820.1785-0.09570.0891-0.0179-0.050.04740.03410.049416.882954.729312.9617
45.0582-0.7566-0.52333.7186-1.51794.31790.03240.41020.4528-0.2432-0.0352-0.2743-0.15040.05490.00280.1708-0.0383-0.00220.04410.0390.056322.705151.144336.134
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A29 - 114
2X-RAY DIFFRACTION2B29 - 114
3X-RAY DIFFRACTION3C27 - 111
4X-RAY DIFFRACTION4D28 - 114

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