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- PDB-3ucp: Outer membrane Endecaheme cytochrome UndA from Shewanella sp. HRCR-6 -

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Basic information

Entry
Database: PDB / ID: 3ucp
TitleOuter membrane Endecaheme cytochrome UndA from Shewanella sp. HRCR-6
ComponentsUndA
KeywordsTRANSPORT PROTEIN / beta-barrel / c-type cytochrome / Electron Transport / c-type hemes / cell surface
Function / homology
Function and homology information


oxidoreductase activity / metal ion binding
Similarity search - Function
: / OmcA-like N-terminal domain / Cytochrome c554 and c-prime / Decahaem cytochrome, c-type, OmcA/MtrC / : / Outer membrane cytochrome MtrC/MtrF-like, domains II/IV / : / Multiheme cytochrome superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Biological speciesShewanella sp. HRCR_06 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.76 Å
AuthorsEdwards, M.J. / Clarke, T.A.
CitationJournal: Structure / Year: 2012
Title: The Crystal Structure of the Extracellular 11-heme Cytochrome UndA Reveals a Conserved 10-heme Motif and Defined Binding Site for Soluble Iron Chelates.
Authors: Edwards, M.J. / Hall, A. / Shi, L. / Fredrickson, J.K. / Zachara, J.M. / Butt, J.N. / Richardson, D.J. / Clarke, T.A.
History
DepositionOct 27, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 30, 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 / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_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_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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UndA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,83820
Polymers92,4851
Non-polymers7,35319
Water23,7441318
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.640, 106.090, 151.650
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein UndA


Mass: 92485.195 Da / Num. of mol.: 1 / Fragment: Soluble domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella sp. HRCR_06 (bacteria) / Gene: undA / Plasmid: pBAD / Production host: Shewanella oneidensis (bacteria) / Strain (production host): MR-1 / References: UniProt: F8UWD6

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Non-polymers , 5 types, 1337 molecules

#2: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1318 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 3.03 Å3/Da / Density % sol: 59.39 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M MES, 50 mM MgCl2, 50 mM NaCl, 15% PEG5K, 20% Glycerol, 25mM 9,10-Anthraquinone 2,6-disulfonate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9762 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 11, 2011 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.76→46.8 Å / Num. obs: 110938 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2.2 / Redundancy: 3.9 % / Rmerge(I) obs: 0.094 / Rsym value: 0.094 / Net I/σ(I): 4.8
Reflection shellResolution: 1.76→1.86 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.332 / Mean I/σ(I) obs: 3.7 / Rsym value: 0.332 / % possible all: 99.3

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Processing

Software
NameVersionClassification
xia2data scaling
SHELXmodel building
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.76→40.91 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.966 / SU ML: 0.053 / Cross valid method: THROUGHOUT / ESU R: 0.084 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1774 5538 5 %RANDOM
Rwork0.14399 ---
obs0.14565 105111 99.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.216 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.76→40.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5948 0 506 1318 7772
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0226706
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.452.1659288
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1395821
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.82125.02251
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.1515957
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.6981519
X-RAY DIFFRACTIONr_chiral_restr0.1280.2953
X-RAY DIFFRACTIONr_gen_planes_refined0.0190.0215171
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.4431.54003
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.17226450
X-RAY DIFFRACTIONr_scbond_it3.32532703
X-RAY DIFFRACTIONr_scangle_it4.8274.52827
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.76→1.81 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.242 413 -
Rwork0.239 7576 -
obs--98.45 %
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)
13.66054.09320.5786.80320.59460.55140.1644-0.33040.02030.449-0.15780.3557-0.0615-0.1486-0.00660.3619-0.15160.00870.24280.03120.061312.78612.70767.5007
20.69240.3936-0.11710.83-0.04230.89830.1752-0.1934-0.08930.3465-0.198-0.16480.01190.04960.02280.2227-0.0847-0.10720.10330.04790.053628.709419.784457.4936
30.54240.14470.20990.8779-0.01560.67690.032-0.0983-0.00020.1528-0.0472-0.1417-0.0167-0.01440.01530.1055-0.0168-0.05830.07320.01420.094630.448827.626740.8763
40.5151-0.10940.30620.4551-0.0840.76160.0103-0.0197-0.03650.0258-0.00720.00090.0379-0.0932-0.00310.0254-0.01530.00530.0791-0.00420.06438.475322.361314.2432
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A44 - 63
2X-RAY DIFFRACTION2A64 - 236
3X-RAY DIFFRACTION3A237 - 462
4X-RAY DIFFRACTION4A463 - 843

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