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- PDB-4n2o: Structure of a novel autonomous cohesin protein from Ruminococcus... -

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Basic information

Entry
Database: PDB / ID: 4n2o
TitleStructure of a novel autonomous cohesin protein from Ruminococcus flavefaciens
ComponentsAutonomous cohesin
KeywordsSTRUCTURAL PROTEIN / Nine-stranded beta sandwich / cohesin / Dockerin
Function / homologyImmunoglobulin-like - #680 / Immunoglobulin-like / Sandwich / Mainly Beta / Autonomous cohesin
Function and homology information
Biological speciesRuminococcus flavefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.442 Å
AuthorsFrolow, F. / Voronov-Goldman, M. / Levy-Assaraf, M. / Lamed, R. / Bayer, E. / Shimon, L.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2014
Title: Structural characterization of a novel autonomous cohesin from Ruminococcus flavefaciens.
Authors: Voronov-Goldman, M. / Levy-Assaraf, M. / Yaniv, O. / Wisserman, G. / Jindou, S. / Borovok, I. / Bayer, E.A. / Lamed, R. / Shimon, L.J. / Frolow, F.
History
DepositionOct 5, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2014Group: Database references
Revision 1.2May 14, 2014Group: Database references
Revision 1.3Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.name ..._software.classification / _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 / _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

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Assembly

Deposited unit
A: Autonomous cohesin
B: Autonomous cohesin
C: Autonomous cohesin
D: Autonomous cohesin
E: Autonomous cohesin
F: Autonomous cohesin
G: Autonomous cohesin
H: Autonomous cohesin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,90712
Polymers182,7658
Non-polymers1424
Water6,900383
1
A: Autonomous cohesin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9173
Polymers22,8461
Non-polymers712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Autonomous cohesin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8812
Polymers22,8461
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Autonomous cohesin


Theoretical massNumber of molelcules
Total (without water)22,8461
Polymers22,8461
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Autonomous cohesin


Theoretical massNumber of molelcules
Total (without water)22,8461
Polymers22,8461
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Autonomous cohesin


Theoretical massNumber of molelcules
Total (without water)22,8461
Polymers22,8461
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Autonomous cohesin


Theoretical massNumber of molelcules
Total (without water)22,8461
Polymers22,8461
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Autonomous cohesin


Theoretical massNumber of molelcules
Total (without water)22,8461
Polymers22,8461
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Autonomous cohesin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8812
Polymers22,8461
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
A: Autonomous cohesin
B: Autonomous cohesin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7985
Polymers45,6912
Non-polymers1063
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-54 kcal/mol
Surface area16560 Å2
MethodPISA
10
C: Autonomous cohesin
D: Autonomous cohesin


Theoretical massNumber of molelcules
Total (without water)45,6912
Polymers45,6912
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2590 Å2
ΔGint-17 kcal/mol
Surface area16970 Å2
MethodPISA
11
E: Autonomous cohesin
F: Autonomous cohesin


Theoretical massNumber of molelcules
Total (without water)45,6912
Polymers45,6912
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2560 Å2
ΔGint-18 kcal/mol
Surface area17290 Å2
MethodPISA
12
G: Autonomous cohesin
H: Autonomous cohesin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7273
Polymers45,6912
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2870 Å2
ΔGint-30 kcal/mol
Surface area16570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.240, 67.726, 258.907
Angle α, β, γ (deg.)90.00, 93.08, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-440-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16A
26G
17A
27H
18B
28C
19B
29D
110B
210E
111B
211F
112B
212G
113B
213H
114C
214D
115C
215E
116C
216F
117C
217G
118C
218H
119D
219E
120D
220F
121D
221G
122D
222H
123E
223F
124E
224G
125E
225H
126F
226G
127F
227H
128G
228H

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERGLUGLUAA4 - 1954 - 195
21SERSERGLUGLUBB4 - 1954 - 195
12ALAALAGLUGLUAA8 - 1958 - 195
22ALAALAGLUGLUCC8 - 1958 - 195
13SERSERGLUGLUAA4 - 1934 - 193
23SERSERGLUGLUDD4 - 1934 - 193
14VALVALLEULEUAA6 - 1946 - 194
24VALVALLEULEUEE6 - 1946 - 194
15THRTHRGLUGLUAA7 - 1957 - 195
25THRTHRGLUGLUFF7 - 1957 - 195
16SERSERGLUGLUAA5 - 1955 - 195
26SERSERGLUGLUGG5 - 1955 - 195
17VALVALGLUGLUAA6 - 1956 - 195
27VALVALGLUGLUHH6 - 1956 - 195
18ALAALAGLUGLUBB8 - 1958 - 195
28ALAALAGLUGLUCC8 - 1958 - 195
19SERSERGLUGLUBB4 - 1934 - 193
29SERSERGLUGLUDD4 - 1934 - 193
110VALVALLEULEUBB6 - 1946 - 194
210VALVALLEULEUEE6 - 1946 - 194
111THRTHRGLUGLUBB7 - 1957 - 195
211THRTHRGLUGLUFF7 - 1957 - 195
112SERSERGLUGLUBB5 - 1955 - 195
212SERSERGLUGLUGG5 - 1955 - 195
113VALVALGLUGLUBB6 - 1956 - 195
213VALVALGLUGLUHH6 - 1956 - 195
114ALAALAGLUGLUCC8 - 1938 - 193
214ALAALAGLUGLUDD8 - 1938 - 193
115ALAALALEULEUCC8 - 1948 - 194
215ALAALALEULEUEE8 - 1948 - 194
116ALAALAHISHISCC8 - 1968 - 196
216ALAALAHISHISFF8 - 1968 - 196
117ALAALAGLUGLUCC8 - 1958 - 195
217ALAALAGLUGLUGG8 - 1958 - 195
118ALAALAGLUGLUCC8 - 1958 - 195
218ALAALAGLUGLUHH8 - 1958 - 195
119VALVALGLUGLUDD6 - 1936 - 193
219VALVALGLUGLUEE6 - 1936 - 193
120THRTHRGLUGLUDD7 - 1937 - 193
220THRTHRGLUGLUFF7 - 1937 - 193
121SERSERGLUGLUDD5 - 1935 - 193
221SERSERGLUGLUGG5 - 1935 - 193
122VALVALGLUGLUDD6 - 1936 - 193
222VALVALGLUGLUHH6 - 1936 - 193
123THRTHRLEULEUEE7 - 1947 - 194
223THRTHRLEULEUFF7 - 1947 - 194
124VALVALLEULEUEE6 - 1946 - 194
224VALVALLEULEUGG6 - 1946 - 194
125VALVALLEULEUEE6 - 1946 - 194
225VALVALLEULEUHH6 - 1946 - 194
126THRTHRGLUGLUFF7 - 1957 - 195
226THRTHRGLUGLUGG7 - 1957 - 195
127THRTHRGLUGLUFF7 - 1957 - 195
227THRTHRGLUGLUHH7 - 1957 - 195
128VALVALGLUGLUGG6 - 1956 - 195
228VALVALGLUGLUHH6 - 1956 - 195

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
Autonomous cohesin


Mass: 22845.656 Da / Num. of mol.: 8 / Fragment: RfCohG module residue numbers 26-218
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruminococcus flavefaciens (bacteria) / Strain: FD-1 / Plasmid: pET28(+) / Production host: Escherichia coli (E. coli) / References: UniProt: W5IDC3*PLUS
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 383 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.78 Å3/Da / Density % sol: 55.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 9 ul drop containing 2 ul of SeMet-RfCohG-CH solution (13mg/ml) and 7 ul reservoir solution (0.1 M Sodium Acetate pH 5 and 6% w/v Polyethylene glycol 4000), VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9762 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 10, 2009 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.44→22.77 Å / Num. all: 72856 / Num. obs: 72856 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Rmerge(I) obs: 0.14 / Rsym value: 0.13 / Net I/σ(I): 24

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
SHELXSphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
DENZOdata reduction
SCALEPACKdata scaling
X-QUBEdata collection
RefinementMethod to determine structure: SAD / Resolution: 2.442→22.77 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.926 / SU B: 18.104 / SU ML: 0.177 / Cross valid method: THROUGHOUT / ESU R: 0.404 / ESU R Free: 0.242 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22889 3678 5.1 %RANDOM
Rwork0.20537 ---
obs0.2066 69119 96.81 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.744 Å2
Baniso -1Baniso -2Baniso -3
1--1.92 Å20 Å20.21 Å2
2---1.32 Å20 Å2
3---3.2 Å2
Refinement stepCycle: LAST / Resolution: 2.442→22.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11858 0 4 383 12245
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01912143
X-RAY DIFFRACTIONr_bond_other_d0.0040.0211088
X-RAY DIFFRACTIONr_angle_refined_deg1.5291.97616488
X-RAY DIFFRACTIONr_angle_other_deg2.166325680
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.29151703
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.03126.547585
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.351151733
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.681516
X-RAY DIFFRACTIONr_chiral_restr0.0810.21798
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02115257
X-RAY DIFFRACTIONr_gen_planes_other0.0040.022783
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_it2.8091.9846147
X-RAY DIFFRACTIONr_mcbond_other2.7991.9846146
X-RAY DIFFRACTIONr_mcangle_it4.212.9617675
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.5322.3565996
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A109080.07
12B109080.07
21A104860.09
22C104860.09
31A104420.09
32D104420.09
41A104760.1
42E104760.1
51A104820.1
52F104820.1
61A108190.07
62G108190.07
71A107140.07
72H107140.07
81B103560.1
82C103560.1
91B106760.09
92D106760.09
101B106980.09
102E106980.09
111B104790.1
112F104790.1
121B108210.08
122G108210.08
131B109840.07
132H109840.07
141C102420.1
142D102420.1
151C103340.11
152E103340.11
161C103630.11
162F103630.11
171C103900.1
172G103900.1
181C102670.1
182H102670.1
191D106640.09
192E106640.09
201D100930.11
202F100930.11
211D103450.1
212G103450.1
221D104020.09
222H104020.09
231E101670.11
232F101670.11
241E102980.11
242G102980.11
251E104620.1
252H104620.1
261F105200.09
262G105200.09
271F105050.1
272H105050.1
281G107950.08
282H107950.08
LS refinement shellResolution: 2.442→2.505 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 183 -
Rwork0.301 3499 -
obs--65.99 %
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)
11.02570.2735-0.61881.5275-0.7311.8283-0.07180.0043-0.06720.0114-0.0131-0.0816-0.03970.10030.08490.18760.0096-0.01890.1886-0.00960.010511.645-0.413127.256
22.43840.0564-0.9911.4730.20331.681-0.15110.1058-0.2021-0.0750.0344-0.04550.1294-0.05880.11670.2798-0.04820.01250.2109-0.04150.024410.67-9.631102.531
31.70470.2143-0.65041.82370.5892.5163-0.0730.34440.0592-0.4672-0.0061-0.0456-0.4068-0.07220.0790.3964-0.0608-0.0310.31690.01770.013929.60818.53189.614
42.45910.9405-0.72352.3815-0.64143.1817-0.18370.1612-0.2358-0.4475-0.0921-0.3725-0.10620.19850.27580.44810.00520.15060.4235-0.04260.10543.5923.71972.729
52.2866-0.36521.28031.7228-0.78673.44310.1074-0.4440.15070.2119-0.1117-0.06820.3595-0.10330.00430.4084-0.0031-0.08880.5442-0.14260.059650.07145.81557.342
62.6973-0.11680.55142.02620.35192.7643-0.0133-0.4743-0.07230.443-0.02170.01980.2984-0.12880.03510.30030.02360.01260.27530.00090.003836.42130.95439.123
71.0539-0.28390.65211.439-0.73191.7537-0.0690.02320.05380.00310.0196-0.06250.02840.12070.04930.1646-0.0021-0.00680.1506-0.00820.00518.43750.5322.071
82.0566-0.2050.68071.1440.1891.2254-0.1328-0.13450.20460.05290.0893-0.0951-0.119-0.02740.04350.26080.0417-0.02590.1958-0.06370.036717.42959.36526.954
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 196
2X-RAY DIFFRACTION1A301
3X-RAY DIFFRACTION1A401 - 474
4X-RAY DIFFRACTION2B4 - 196
5X-RAY DIFFRACTION2B301
6X-RAY DIFFRACTION2B401 - 458
7X-RAY DIFFRACTION3C8 - 197
8X-RAY DIFFRACTION3C301 - 351
9X-RAY DIFFRACTION4D4 - 194
10X-RAY DIFFRACTION4D301 - 306
11X-RAY DIFFRACTION5E6 - 195
12X-RAY DIFFRACTION5E301 - 308
13X-RAY DIFFRACTION6F7 - 199
14X-RAY DIFFRACTION6F301 - 353
15X-RAY DIFFRACTION7G5 - 196
16X-RAY DIFFRACTION7G301 - 369
17X-RAY DIFFRACTION8H6 - 196
18X-RAY DIFFRACTION8H301
19X-RAY DIFFRACTION8H401 - 464

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