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- PDB-4qo5: Hypothetical multiheme protein -

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Basic information

Entry
Database: PDB / ID: 4qo5
TitleHypothetical multiheme protein
ComponentsHypothetical multiheme protein
KeywordsHEME BINDING PROTEIN / multi-heme protein / membrane anchor
Function / homologyCytochrome c-552/4 / Cytochrome c554 and c-prime / Seven times multi-haem cytochrome CxxCH / Multiheme cytochrome superfamily / metal ion binding / HEME C / Cytochrome c-552/4 domain-containing protein
Function and homology information
Biological speciesIgnicoccus hospitalis KIN4/I (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.697 Å
AuthorsRajendran, C.
CitationJournal: Febs J. / Year: 2016
Title: In meso crystal structure of a novel membrane-associated octaheme cytochrome c from the Crenarchaeon Ignicoccus hospitalis.
Authors: Parey, K. / Fielding, A.J. / Sorgel, M. / Rachel, R. / Huber, H. / Ziegler, C. / Rajendran, C.
History
DepositionJun 19, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2016Group: Database references / Source and taxonomy
Revision 1.2Nov 23, 2016Group: Database references
Revision 1.3May 23, 2018Group: Advisory / Data collection / Derived calculations
Category: pdbx_distant_solvent_atoms / struct_conn / struct_conn_type
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Nov 27, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypothetical multiheme protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,49011
Polymers58,2811
Non-polymers5,20910
Water7,332407
1
A: Hypothetical multiheme protein
hetero molecules

A: Hypothetical multiheme protein
hetero molecules

A: Hypothetical multiheme protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)190,47133
Polymers174,8433
Non-polymers15,62830
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area48920 Å2
ΔGint-705 kcal/mol
Surface area47050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.440, 136.440, 214.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-743-

HOH

21A-1030-

HOH

31A-1035-

HOH

41A-1054-

HOH

51A-1060-

HOH

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Components

#1: Protein Hypothetical multiheme protein


Mass: 58280.895 Da / Num. of mol.: 1 / Fragment: UNP residues 29-549 / Source method: isolated from a natural source / Source: (natural) Ignicoccus hospitalis KIN4/I (archaea) / References: UniProt: A8AB33
#2: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 8 / 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: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 407 / 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: 3.3 Å3/Da / Density % sol: 62.76 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.7 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7 Å / Relative weight: 1
ReflectionResolution: 1.697→43.726 Å / Num. all: 84827 / Num. obs: 84427 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellHighest resolution: 1.697 Å

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.1_1168) / Classification: refinement
RefinementMethod to determine structure: SAD / Resolution: 1.697→43.726 Å / SU ML: 0.2 / σ(F): 1.99 / Phase error: 23.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2009 4212 5 %
Rwork0.165 --
obs0.1668 84427 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.697→43.726 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4054 0 359 407 4820
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114579
X-RAY DIFFRACTIONf_angle_d1.546353
X-RAY DIFFRACTIONf_dihedral_angle_d16.5541562
X-RAY DIFFRACTIONf_chiral_restr0.078642
X-RAY DIFFRACTIONf_plane_restr0.009770
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.697-1.71640.4582360.39824490X-RAY DIFFRACTION86
1.7164-1.73650.31782740.31445212X-RAY DIFFRACTION100
1.7365-1.75770.34862760.29725200X-RAY DIFFRACTION100
1.7577-1.780.29582820.27215273X-RAY DIFFRACTION100
1.78-1.80340.23852730.25275206X-RAY DIFFRACTION100
1.8034-1.82810.30332760.24735182X-RAY DIFFRACTION100
1.8281-1.85420.25792740.2415212X-RAY DIFFRACTION100
1.8542-1.88190.27532780.22515233X-RAY DIFFRACTION100
1.8819-1.91130.27042760.2245202X-RAY DIFFRACTION100
1.9113-1.94260.28772770.23915225X-RAY DIFFRACTION100
1.9426-1.97610.25932770.1975256X-RAY DIFFRACTION100
1.9761-2.01210.21062750.18635208X-RAY DIFFRACTION100
2.0121-2.05080.21882750.18375235X-RAY DIFFRACTION100
2.0508-2.09260.21582750.17945203X-RAY DIFFRACTION100
2.0926-2.13810.20422770.17325235X-RAY DIFFRACTION100
2.1381-2.18790.20272740.16385185X-RAY DIFFRACTION100
2.1879-2.24260.212740.17425194X-RAY DIFFRACTION100
2.2426-2.30320.23022750.17565199X-RAY DIFFRACTION100
2.3032-2.3710.18882740.15215246X-RAY DIFFRACTION100
2.371-2.44750.19212760.15545220X-RAY DIFFRACTION100
2.4475-2.5350.22212740.15735214X-RAY DIFFRACTION100
2.535-2.63650.1962790.15555211X-RAY DIFFRACTION100
2.6365-2.75640.21182740.15545206X-RAY DIFFRACTION100
2.7564-2.90170.18042770.15945227X-RAY DIFFRACTION100
2.9017-3.08350.20552710.16275197X-RAY DIFFRACTION99
3.0835-3.32150.19752670.15275213X-RAY DIFFRACTION100
3.3215-3.65560.16382690.14185241X-RAY DIFFRACTION100
3.6556-4.18420.15382680.12825214X-RAY DIFFRACTION100
4.1842-5.27020.15232750.12365244X-RAY DIFFRACTION100
5.2702-43.74070.17822760.14045196X-RAY DIFFRACTION99
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)
12.4550.6059-0.55130.6671-0.09650.8732-0.07170.3735-0.183-0.17530.0767-0.06630.1685-0.01750.01130.2364-0.00570.01240.2331-0.03180.2156-45.853225.2099-28.6847
20.4810.0465-0.11680.40580.13390.9637-0.01080.0086-0.00890.00030.0235-0.1023-0.00360.1833-0.02580.13540.0007-0.01050.20720.00290.2143-38.275938.1884-13.2834
31.5945-0.2112-0.31511.16950.58471.38280.0065-0.2346-0.35870.19070.0137-0.03720.28630.04590.01970.2627-0.0127-0.06160.24660.04640.2575-44.464626.19667.7206
41.1610.28440.43850.52080.09911.4657-0.01340.017-0.150.00870.0052-0.14830.14160.1562-0.01490.15290.0273-0.00650.18780.00350.1923-42.102430.4583-8.1027
50.85460.0045-0.09930.32620.05170.85580.02060.00470.03410.0383-0.0124-0.0541-0.04110.00380.00160.151-0.0049-0.00510.1411-0.00930.2098-54.978951.4306-7.9986
60.8182-0.2751-1.01220.2262-0.12912.88670.0756-0.72460.35520.45970.0142-0.12020.06460.2595-0.03210.456-0.0782-0.05720.5813-0.11880.3227-44.738856.862926.5888
71.3046-0.11831.10850.4305-0.28061.0118-0.2428-0.01570.31890.1589-0.0318-0.1432-0.37140.16990.24480.2875-0.0287-0.03190.2586-0.04090.34-47.529163.5444.8096
80.7298-0.55321.19631.2334-1.7563.8078-0.0547-0.11580.11740.25760.0175-0.064-0.33530.13640.04120.2548-0.0187-0.010.2685-0.05440.2512-59.098859.325113.7434
90.9733-0.1202-0.18470.9566-0.42920.85480.0103-0.2029-0.00550.17080.0454-0.0405-0.0264-0.0021-0.06530.199-0.0175-0.01380.2164-0.03440.1788-60.839146.990619.7377
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 29 through 58 )
2X-RAY DIFFRACTION2chain 'A' and (resid 59 through 175 )
3X-RAY DIFFRACTION3chain 'A' and (resid 176 through 213 )
4X-RAY DIFFRACTION4chain 'A' and (resid 214 through 253 )
5X-RAY DIFFRACTION5chain 'A' and (resid 254 through 361 )
6X-RAY DIFFRACTION6chain 'A' and (resid 362 through 396 )
7X-RAY DIFFRACTION7chain 'A' and (resid 397 through 440 )
8X-RAY DIFFRACTION8chain 'A' and (resid 441 through 475 )
9X-RAY DIFFRACTION9chain 'A' and (resid 476 through 549 )

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