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- PDB-4ow1: Crystal Structure of Resuscitation Promoting Factor C -

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Basic information

Entry
Database: PDB / ID: 4ow1
TitleCrystal Structure of Resuscitation Promoting Factor C
ComponentsResuscitation-promoting factor RpfC
KeywordsHYDROLASE / Resuscitation Promoting Factor / Peptidoglycan / Transglycosylase
Function / homology
Function and homology information


Hydrolases / quorum sensing / regulation of cell population proliferation / hydrolase activity / negative regulation of gene expression / positive regulation of gene expression / extracellular region
Similarity search - Function
Resuscitation-promoting factor, core lysozyme-like domain / Transglycosylase-like domain / Lysozyme - #10 / Lysozyme / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Resuscitation-promoting factor RpfC
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å
AuthorsChauviac, F.X. / Quay, D.H.X. / Cohen-Gonsaud, M. / Keep, N.H.
Funding support United Kingdom, France, European Union, 5items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)G0401038 United Kingdom
FRISBIANR-10-INSB-05-01 France
European Union (EU)X-TBEuropean Union
Bloomsbury StudentshipFXC United Kingdom
Commonwealth Study CommisionMYCS-2011-252 United Kingdom
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2014
Title: The RpfC (Rv1884) atomic structure shows high structural conservation within the resuscitation-promoting factor catalytic domain.
Authors: Chauviac, F.X. / Robertson, G. / Quay, D.H. / Bagneris, C. / Dumas, C. / Henderson, B. / Ward, J. / Keep, N.H. / Cohen-Gonsaud, M.
History
DepositionJan 29, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 18, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 13, 2014Group: Database references
Revision 1.2Feb 4, 2015Group: Derived calculations
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Derived calculations ...Author supporting evidence / Derived calculations / Other / Source and taxonomy / Structure summary
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_keywords / struct_site / symmetry
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text / _struct_site.details / _symmetry.Int_Tables_number
Revision 1.4Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support
Item: _pdbx_audit_support.country / _pdbx_audit_support.funding_organization
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Resuscitation-promoting factor RpfC
B: Resuscitation-promoting factor RpfC
E: Resuscitation-promoting factor RpfC
X: Resuscitation-promoting factor RpfC
W: Resuscitation-promoting factor RpfC
T: Resuscitation-promoting factor RpfC
S: Resuscitation-promoting factor RpfC
U: Resuscitation-promoting factor RpfC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,63110
Polymers74,5068
Non-polymers1242
Water4,179232
1
A: Resuscitation-promoting factor RpfC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,3752
Polymers9,3131
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Resuscitation-promoting factor RpfC


Theoretical massNumber of molelcules
Total (without water)9,3131
Polymers9,3131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
E: Resuscitation-promoting factor RpfC


Theoretical massNumber of molelcules
Total (without water)9,3131
Polymers9,3131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
X: Resuscitation-promoting factor RpfC


Theoretical massNumber of molelcules
Total (without water)9,3131
Polymers9,3131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
W: Resuscitation-promoting factor RpfC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,3752
Polymers9,3131
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
T: Resuscitation-promoting factor RpfC


Theoretical massNumber of molelcules
Total (without water)9,3131
Polymers9,3131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
S: Resuscitation-promoting factor RpfC


Theoretical massNumber of molelcules
Total (without water)9,3131
Polymers9,3131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
U: Resuscitation-promoting factor RpfC


Theoretical massNumber of molelcules
Total (without water)9,3131
Polymers9,3131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.230, 89.930, 78.090
Angle α, β, γ (deg.)90.00, 115.08, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22E
13A
23X
14A
24W
15A
25T
16A
26S
17A
27U
18B
28E
19B
29X
110B
210W
111B
211T
112B
212S
113B
213U
114E
214X
115E
215W
116E
216T
117E
217S
118E
218U
119X
219W
120X
220T
121X
221S
122X
222U
123W
223T
124W
224S
125W
225U
126T
226S
127T
227U
128S
228U

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROSERSERAA4 - 774 - 77
21PROPROSERSERBB4 - 774 - 77
12GLYGLYLYSLYSAA1 - 861 - 86
22GLYGLYLYSLYSEC1 - 861 - 86
13SERSERLEULEUAA3 - 793 - 79
23SERSERLEULEUXD3 - 793 - 79
14GLYGLYLEULEUAA1 - 831 - 83
24GLYGLYLEULEUWE1 - 831 - 83
15GLYGLYTRPTRPAA1 - 841 - 84
25GLYGLYTRPTRPTF1 - 841 - 84
16GLYGLYLYSLYSAA1 - 861 - 86
26GLYGLYLYSLYSSG1 - 861 - 86
17PROPROSERSERAA2 - 852 - 85
27PROPROSERSERUH2 - 852 - 85
18PROPROSERSERBB4 - 774 - 77
28PROPROSERSEREC4 - 774 - 77
19PROPROSERSERBB4 - 774 - 77
29PROPROSERSERXD4 - 774 - 77
110PROPROSERSERBB4 - 774 - 77
210PROPROSERSERWE4 - 774 - 77
111PROPROSERSERBB4 - 774 - 77
211PROPROSERSERTF4 - 774 - 77
112PROPROSERSERBB4 - 774 - 77
212PROPROSERSERSG4 - 774 - 77
113PROPROSERSERBB4 - 774 - 77
213PROPROSERSERUH4 - 774 - 77
114SERSERLEULEUEC3 - 793 - 79
214SERSERLEULEUXD3 - 793 - 79
115GLYGLYLEULEUEC1 - 831 - 83
215GLYGLYLEULEUWE1 - 831 - 83
116GLYGLYTRPTRPEC1 - 841 - 84
216GLYGLYTRPTRPTF1 - 841 - 84
117GLYGLYLYSLYSEC1 - 861 - 86
217GLYGLYLYSLYSSG1 - 861 - 86
118PROPROSERSEREC2 - 852 - 85
218PROPROSERSERUH2 - 852 - 85
119SERSERLEULEUXD3 - 793 - 79
219SERSERLEULEUWE3 - 793 - 79
120SERSERLEULEUXD3 - 793 - 79
220SERSERLEULEUTF3 - 793 - 79
121SERSERLEULEUXD3 - 793 - 79
221SERSERLEULEUSG3 - 793 - 79
122SERSERLEULEUXD3 - 793 - 79
222SERSERLEULEUUH3 - 793 - 79
123GLYGLYLEULEUWE1 - 831 - 83
223GLYGLYLEULEUTF1 - 831 - 83
124GLYGLYLEULEUWE1 - 831 - 83
224GLYGLYLEULEUSG1 - 831 - 83
125PROPROLEULEUWE2 - 832 - 83
225PROPROLEULEUUH2 - 832 - 83
126GLYGLYTRPTRPTF1 - 841 - 84
226GLYGLYTRPTRPSG1 - 841 - 84
127PROPROTRPTRPTF2 - 842 - 84
227PROPROTRPTRPUH2 - 842 - 84
128PROPROSERSERSG2 - 852 - 85
228PROPROSERSERUH2 - 852 - 85

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28

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Components

#1: Protein
Resuscitation-promoting factor RpfC


Mass: 9313.296 Da / Num. of mol.: 8 / Fragment: UNP residues 68-159
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rva / Gene: MTCY180.34,Rv1884c,rpfC / Plasmid: pET15bTEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O07747, Hydrolases
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 232 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.82 Å3/Da / Density % sol: 56.6 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 0.1 M NaCitrate pH 5, 22% (w/v) PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0723 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 6, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0723 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.536
11-H, -K, H+L20.464
ReflectionResolution: 1.9→44.97 Å / Num. all: 64809 / Num. obs: 64089 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 8.3
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.382 / Mean I/σ(I) obs: 2.6 / % possible all: 100

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Processing

SoftwareName: REFMAC / Version: 5.8.0049 / Classification: refinement
RefinementResolution: 1.9→38.42 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.936 / SU B: 3.95 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.029 / ESU R Free: 0.027 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23548 3271 5 %RANDOM
Rwork0.20502 ---
obs0.20653 61793 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.634 Å2
Baniso -1Baniso -2Baniso -3
1-29.72 Å20 Å215.41 Å2
2---19.78 Å20 Å2
3----9.94 Å2
Refinement stepCycle: 1 / Resolution: 1.9→38.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4741 0 8 232 4981
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.024919
X-RAY DIFFRACTIONr_bond_other_d0.0140.024397
X-RAY DIFFRACTIONr_angle_refined_deg1.8231.9036742
X-RAY DIFFRACTIONr_angle_other_deg1.7423.00210063
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6615669
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.01425.437206
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.92315590
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0031516
X-RAY DIFFRACTIONr_chiral_restr0.1190.2677
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0216015
X-RAY DIFFRACTIONr_gen_planes_other0.0110.021201
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_it2.0871.8622667
X-RAY DIFFRACTIONr_mcbond_other2.0831.8622666
X-RAY DIFFRACTIONr_mcangle_it2.7342.7833324
X-RAY DIFFRACTIONr_mcangle_other2.7342.7833325
X-RAY DIFFRACTIONr_scbond_it2.2532.0132252
X-RAY DIFFRACTIONr_scbond_other2.2542.0142253
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0672.9573414
X-RAY DIFFRACTIONr_long_range_B_refined4.22915.6865863
X-RAY DIFFRACTIONr_long_range_B_other4.2315.695864
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A36710.03
12B36710.03
21A41790.08
22E41790.08
31A38070.04
32X38070.04
41A40640.05
42W40640.05
51A40940.08
52T40940.08
61A41890.08
62S41890.08
71A41640.06
72U41640.06
81B36270.04
82E36270.04
91B36560.02
92X36560.02
101B36490.02
102W36490.02
111B35970.05
112T35970.05
121B36430.04
122S36430.04
131B36470.03
132U36470.03
141E37990.05
142X37990.05
151E40800.06
152W40800.06
161E42110.05
162T42110.05
171E41980.08
172S41980.08
181E41820.07
182U41820.07
191X38160.04
192W38160.04
201X37590.05
202T37590.05
211X38090.05
212S38090.05
221X38030.05
222U38030.05
231W40430.07
232T40430.07
241W40810.07
242S40810.07
251W40620.06
252U40620.06
261T41380.07
262S41380.07
271T41000.08
272U41000.08
281S41400.08
282U41400.08
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 271 -
Rwork0.216 4462 -
obs--99.2 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.3122-0.53820.40214.1517-1.94673.3106-0.02570.30410.2101-0.22870.0462-0.0216-0.21110.029-0.02040.0579-0.01760.00580.04870.02240.026640.909215.13427.2974
22.1264-0.286-0.45314.466-0.7612.47230.00770.32670.1616-0.4269-0.0509-0.0762-0.09780.01960.04320.0595-0.01310.00930.07890.03430.07269.980514.01751.0657
32.15720.6021-0.68173.9982-1.73632.63460.0872-0.3739-0.21870.39640.0007-0.15780.17660.0699-0.0880.1117-0.0036-0.05570.07730.02940.056640.9462-13.617531.9093
42.27440.54-0.87364.9954-0.29633.3136-0.0598-0.29310.12030.59350.0713-0.0397-0.19710.0343-0.01150.09680.0281-0.00160.0687-0.01950.04164.504510.851423.7808
52.79910.6362-0.07923.97130.45562.5706-0.0107-0.41010.17230.49520.0311-0.0186-0.28050.0269-0.02050.1140.0237-0.00570.0804-0.0310.031338.942611.532531.8155
63.6997-0.68130.72563.88290.40552.264-0.02030.4249-0.1525-0.46370.12020.05680.26080.0468-0.09990.1124-0.0384-0.01420.0636-0.01510.010139.2607-10.20047.3235
73.3092-1.42710.35882.54640.38621.05840.02510.4913-0.1654-0.22570.00970.15110.2858-0.0443-0.03470.1738-0.08980.00360.1484-0.03670.08786.8385-10.2981-0.3439
81.71610.4365-0.56163.5489-1.55241.94690.0759-0.2921-0.24490.1622-0.0076-0.21040.21160.0808-0.06820.11310.0073-0.03990.09390.03730.11088.0692-13.615724.4319
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 86
2X-RAY DIFFRACTION2B4 - 78
3X-RAY DIFFRACTION3E1 - 86
4X-RAY DIFFRACTION4X3 - 80
5X-RAY DIFFRACTION5W1 - 84
6X-RAY DIFFRACTION6T1 - 85
7X-RAY DIFFRACTION7S1 - 85
8X-RAY DIFFRACTION8U2 - 86

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