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- PDB-5xdh: His/DOPA ligated cytochrome c from an anammox organism KSU-1 -

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Basic information

Entry
Database: PDB / ID: 5xdh
TitleHis/DOPA ligated cytochrome c from an anammox organism KSU-1
ComponentsPutative cytochrome c
KeywordsELECTRON TRANSPORT / Cytochrome c / ET protein / DOPA ligand
Function / homologyCytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / electron transfer activity / heme binding / metal ion binding / ACETATE ION / HEME C / Putative cytochrome c
Function and homology information
Biological speciesCandidatus Jettenia caeni (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.32 Å
AuthorsHira, D. / Kitamura, R. / Nakamura, T. / Yamagata, Y. / Furukawa, K. / Fujii, T.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science25850076 Japan
Japan Society for the Promotion of Science26450105 Japan
Kato Memorial Bioscience Foundation Japan
CitationJournal: J. Mol. Biol. / Year: 2018
Title: Anammox Organism KSU-1 Expresses a Novel His/DOPA Ligated Cytochrome c.
Authors: Hira, D. / Kitamura, R. / Nakamura, T. / Yamagata, Y. / Furukawa, K. / Fujii, T.
History
DepositionMar 28, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 28, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 11, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Oct 2, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_comp_id

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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)40,36213
Polymers37,4824
Non-polymers2,8809
Water9,224512
1
A: Putative cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,2035
Polymers9,3701
Non-polymers8334
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-23 kcal/mol
Surface area5240 Å2
MethodPISA
2
B: Putative cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,0853
Polymers9,3701
Non-polymers7152
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-23 kcal/mol
Surface area5150 Å2
MethodPISA
3
C: Putative cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,9892
Polymers9,3701
Non-polymers6191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1150 Å2
ΔGint-23 kcal/mol
Surface area5050 Å2
MethodPISA
4
D: Putative cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,0853
Polymers9,3701
Non-polymers7152
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1300 Å2
ΔGint-35 kcal/mol
Surface area5190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.794, 47.687, 48.993
Angle α, β, γ (deg.)96.460, 99.010, 102.130
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Putative cytochrome c


Mass: 9370.376 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candidatus Jettenia caeni (bacteria) / Strain: KSU-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: I3IL56
#2: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 512 / 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: 2.55 Å3/Da / Density % sol: 51.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 3.2M ammonium sulfate, 200mM Potassium sodium tartrate, 100mM Sodium acetate

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL44XU10.9
SYNCHROTRONSPring-8 BL44XU21.7
Detector
TypeIDDetectorDate
RAYONIX MX300HE1CCDDec 11, 2016
RAYONIX MX300HE2CCDMay 14, 2014
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.91
21.71
ReflectionResolution: 1.32→50 Å / Num. obs: 83160 / % possible obs: 96.3 % / Redundancy: 4 % / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.026 / Rrim(I) all: 0.051 / Χ2: 1.804 / Net I/σ(I): 16
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.32-1.3440.3040.9420.1760.3511.44894.1
1.34-1.3740.2780.9450.1610.3221.47594.2
1.37-1.3940.2480.950.1440.2871.54294.5
1.39-1.4240.2140.9680.1240.2471.50594.8
1.42-1.4540.20.9670.1160.2311.58594.9
1.45-1.4940.1760.9750.1020.2041.63895.3
1.49-1.5240.1470.9820.0850.171.6495.3
1.52-1.5740.1290.9840.0750.1491.72895.8
1.57-1.6140.1150.9890.0670.1331.69995.8
1.61-1.6640.1040.990.060.121.75696.1
1.66-1.7240.0930.9920.0540.1071.77996.4
1.72-1.7940.0770.9840.0450.091.83696.6
1.79-1.8740.0630.9960.0370.0731.91196.9
1.87-1.9740.0550.9960.0320.0641.97897.2
1.97-2.140.0480.9970.0280.0562.06397.5
2.1-2.2640.0410.9980.0240.0482.03797.7
2.26-2.4840.0390.990.0230.0462.09898.1
2.48-2.8440.0350.9980.020.042.15698.5
2.84-3.5840.030.9990.0170.0352.08798.9
3.58-503.90.0280.9980.0170.0332.06696.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data scaling
PDB_EXTRACT3.22data extraction
AutoSolphasing
HKLdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.32→47.84 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.387 / SU ML: 0.029 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.049 / ESU R Free: 0.05
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1752 4109 4.9 %RANDOM
Rwork0.1549 ---
obs0.1559 79049 96.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso max: 48.39 Å2 / Biso mean: 14.807 Å2 / Biso min: 6.77 Å2
Baniso -1Baniso -2Baniso -3
1--0.66 Å2-0.17 Å2-0.36 Å2
2--0.23 Å2-0.09 Å2
3---0.59 Å2
Refinement stepCycle: final / Resolution: 1.32→47.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2610 0 195 512 3317
Biso mean--11.76 28.29 -
Num. residues----343
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.023093
X-RAY DIFFRACTIONr_bond_other_d0.0030.022732
X-RAY DIFFRACTIONr_angle_refined_deg1.8222.0824251
X-RAY DIFFRACTIONr_angle_other_deg1.263.0026416
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3245400
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.36826.842133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.01115529
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.044158
X-RAY DIFFRACTIONr_chiral_restr0.1280.2431
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0213568
X-RAY DIFFRACTIONr_gen_planes_other0.0150.02596
LS refinement shellResolution: 1.322→1.356 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.203 260 -
Rwork0.185 5598 -
all-5858 -
obs--91.56 %
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)
10.68930.119-0.0390.2410.06950.0331-0.020.00630.0623-0.00920.0190.00830.01040.00180.0010.0340.00320.00920.03320.00230.02477.883915.2814-5.5503
20.32530.10530.26850.32290.24850.80310.0547-0.0169-0.0116-0.0235-0.0143-0.02850.00470.0152-0.04040.03390.00210.00540.04280.00290.003810.2112-1.319915.1444
30.9982-0.2120.32580.11550.03060.31790.00660.0468-0.06510.02280.01450.01860.01440.0132-0.02120.02850.0098-0.00610.03360.00790.0287-11.56983.1399-13.3015
40.32710.29980.09740.4980.26260.355-0.0005-0.0135-0.00550.0036-0.0496-0.0072-0.0216-0.01070.050.02470.00630.00330.02280.00180.0301-5.6552-16.3714.472
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 101
2X-RAY DIFFRACTION2B1 - 101
3X-RAY DIFFRACTION3C1 - 101
4X-RAY DIFFRACTION4D1 - 101

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