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- PDB-3cis: The Crystal Structure of Rv2623 from Mycobacterium tuberculosis -

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Basic information

Entry
Database: PDB / ID: 3cis
TitleThe Crystal Structure of Rv2623 from Mycobacterium tuberculosis
ComponentsUncharacterized protein
KeywordsUNKNOWN FUNCTION / alpha/beta hydrolase / ATP / universal stress protein
Function / homology
Function and homology information


dormancy entry of symbiont in host / regulation of growth / peptidoglycan-based cell wall / response to hypoxia / ATP binding / plasma membrane / cytosol
Similarity search - Function
Rossmann fold - #12370 / Universal stress protein A family / UspA / Universal stress protein family / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Universal stress protein MT2698 / Universal stress protein Rv2623
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.9 Å
AuthorsBilder, P. / Drumm, J. / Mi, K. / Chan, J. / Almo, S.C.
CitationJournal: To be Published
Title: The Crystal Structure of Rv2623 : a Novel, Tandem-Repeat Universal Stress Protein of Mycobacterium tuberculosis
Authors: Drumm, J. / Mi, K. / Bilder, P. / Almo, S.C. / Chan, J.
History
DepositionMar 11, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Jul 29, 2020Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.name / _citation_author.name ..._audit_author.name / _citation_author.name / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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: Uncharacterized protein
B: Uncharacterized protein
C: Uncharacterized protein
D: Uncharacterized protein
E: Uncharacterized protein
F: Uncharacterized protein
G: Uncharacterized protein
H: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)273,22940
Polymers264,7258
Non-polymers8,50432
Water6,467359
1
A: Uncharacterized protein
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,30710
Polymers66,1812
Non-polymers2,1268
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8220 Å2
ΔGint-90 kcal/mol
Surface area23490 Å2
MethodPISA
2
C: Uncharacterized protein
D: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,30710
Polymers66,1812
Non-polymers2,1268
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8230 Å2
ΔGint-90 kcal/mol
Surface area23510 Å2
MethodPISA
3
E: Uncharacterized protein
F: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,30710
Polymers66,1812
Non-polymers2,1268
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7300 Å2
ΔGint-83 kcal/mol
Surface area23700 Å2
MethodPISA
4
G: Uncharacterized protein
H: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,30710
Polymers66,1812
Non-polymers2,1268
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7740 Å2
ΔGint-87 kcal/mol
Surface area23770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)172.975, 241.480, 241.659
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
31E
41G
12A
22C
32E
42G
13A
23C
33E
43G
14B
24D
34F
44H
15B
25D
35F
45H
16B
26D
36F
46H

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1112AA8 - 458 - 45
2112CC8 - 458 - 45
3112EE8 - 458 - 45
4112GG8 - 458 - 45
1212AA88 - 14788 - 147
2212CC88 - 14788 - 147
3212EE88 - 14788 - 147
4212GG88 - 14788 - 147
1312AA162 - 201162 - 201
2312CC162 - 201162 - 201
3312EE162 - 201162 - 201
4312GG162 - 201162 - 201
1412AA231 - 250231 - 250
2412CC231 - 250231 - 250
3412EE231 - 250231 - 250
4412GG231 - 250231 - 250
1512AA258 - 293258 - 293
2512CC258 - 293258 - 293
3512EE258 - 293258 - 293
4512GG258 - 293258 - 293
1124AA60 - 8760 - 87
2124CC60 - 8760 - 87
3124EE60 - 8760 - 87
4124GG60 - 8760 - 87
1224AA148 - 161148 - 161
2224CC148 - 161148 - 161
3224EE148 - 161148 - 161
4224GG148 - 161148 - 161
1324AA212 - 222212 - 222
2324CC212 - 222212 - 222
3324EE212 - 222212 - 222
4324GG212 - 222212 - 222
1424AA224 - 229224 - 229
2424CC224 - 229224 - 229
3424EE224 - 229224 - 229
4424GG224 - 229224 - 229
1524AA251 - 257251 - 257
2524CC251 - 257251 - 257
3524EE251 - 257251 - 257
4524GG251 - 257251 - 257
1135AA46 - 5946 - 59
2135CC46 - 5946 - 59
3135EE46 - 5946 - 59
4135GG46 - 5946 - 59
1235AA202 - 211202 - 211
2235CC202 - 211202 - 211
3235EE202 - 211202 - 211
4235GG202 - 211202 - 211
1142BB8 - 458 - 45
2142DD8 - 458 - 45
3142FF8 - 458 - 45
4142HH8 - 458 - 45
1242BB88 - 14788 - 147
2242DD88 - 14788 - 147
3242FF88 - 14788 - 147
4242HH88 - 14788 - 147
1342BB162 - 201162 - 201
2342DD162 - 201162 - 201
3342FF162 - 201162 - 201
4342HH162 - 201162 - 201
1442BB231 - 250231 - 250
2442DD231 - 250231 - 250
3442FF231 - 250231 - 250
4442HH231 - 250231 - 250
1542BB258 - 293258 - 293
2542DD258 - 293258 - 293
3542FF258 - 293258 - 293
4542HH258 - 293258 - 293
1154BB60 - 6760 - 67
2154DD60 - 6760 - 67
3154FF60 - 6760 - 67
4154HH60 - 6760 - 67
1254BB148 - 154148 - 154
2254DD148 - 154148 - 154
3254FF148 - 154148 - 154
4254HH148 - 154148 - 154
1354BB160 - 161160 - 161
2354DD160 - 161160 - 161
3354FF160 - 161160 - 161
4354HH160 - 161160 - 161
1454BB212 - 222212 - 222
2454DD212 - 222212 - 222
3454FF212 - 222212 - 222
4454HH212 - 222212 - 222
1554BB224 - 229224 - 229
2554DD224 - 229224 - 229
3554FF224 - 229224 - 229
4554HH224 - 229224 - 229
1654BB251 - 257251 - 257
2654DD251 - 257251 - 257
3654FF251 - 257251 - 257
4654HH251 - 257251 - 257
1165BB46 - 4746 - 47
2165DD46 - 4746 - 47
3165FF46 - 4746 - 47
4165HH46 - 4746 - 47
1265BB57 - 5957 - 59
2265DD57 - 5957 - 59
3265FF57 - 5957 - 59
4265HH57 - 5957 - 59
1365BB202 - 211202 - 211
2365DD202 - 211202 - 211
3365FF202 - 211202 - 211
4365HH202 - 211202 - 211

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Uncharacterized protein / Universal stress protein family


Mass: 33090.594 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: K-12 / Gene: TB31.7 / Plasmid: pQE-80L / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O06189, UniProt: P9WFD7*PLUS
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 359 / 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: 4.78 Å3/Da / Density % sol: 74.25 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.4
Details: 29% polyacrylate 5100, 100mM sodium citrate, 20mM MgCl2, 200mM MES, pH 5.4, vapor diffusion, sitting drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 10, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 121857 / Num. obs: 121857 / % possible obs: 98.1 % / Redundancy: 5 % / Rsym value: 0.088 / Net I/σ(I): 14.4
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.508 / Mean I/σ(I) obs: 2.013 / Rsym value: 0.508 / % possible all: 95.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4 Å49.58 Å
Translation4 Å49.58 Å
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 124194
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
15.18-10031.80.646847
10.73-15.1827.30.8311510
8.76-10.73240.8841903
7.59-8.7626.90.8842257
6.79-7.5928.20.8512518
6.2-6.7929.10.8392773
5.74-6.227.20.8393028
5.37-5.7425.40.8643246
5.06-5.3725.30.843427
4.8-5.0621.90.8823611
4.58-4.819.90.8993818
4.38-4.5819.70.8893967
4.21-4.3821.40.8844146
4.06-4.2122.70.884303
3.92-4.0626.10.8514410
3.79-3.9226.50.8224634
3.68-3.7924.50.8444730
3.58-3.6824.60.8444876
3.48-3.5825.50.8595020
3.39-3.4825.40.8215118
3.31-3.3927.30.8185264
3.24-3.3126.60.8325405
3.16-3.2427.40.8445485
3.1-3.1628.60.8085631
3.04-3.128.70.8145733
2.98-3.0429.90.7925865
2.92-2.9831.30.7985989
2.87-2.9234.90.7656068
2.8-2.8741.90.6988612

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
DM6phasing
REFMAC5.3.0034refinement
PDB_EXTRACT3.004data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TQ8

1tq8


Resolution: 2.9→49.57 Å / Cor.coef. Fo:Fc: 0.894 / Cor.coef. Fo:Fc free: 0.887 / SU B: 12.897 / SU ML: 0.246 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R: 0.551 / ESU R Free: 0.329 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26817 5560 5 %RANDOM
Rwork0.25047 ---
obs0.25136 105356 99.02 %-
all-121857 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 48.106 Å2
Baniso -1Baniso -2Baniso -3
1-4.57 Å20 Å20 Å2
2---2.96 Å20 Å2
3----1.61 Å2
Refinement stepCycle: LAST / Resolution: 2.9→49.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17267 0 512 359 18138
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02218163
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9791.99224973
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.58552289
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.25823.067714
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.893152711
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.84915168
X-RAY DIFFRACTIONr_chiral_restr0.0540.22948
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213594
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2320.38748
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3170.512437
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.51070
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.230.369
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3370.518
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.637211636
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.272318520
X-RAY DIFFRACTIONr_scbond_it0.71927385
X-RAY DIFFRACTIONr_scangle_it1.24236453
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A776tight positional0.020.05
1A776tight positional0.020
1A776tight positional0.020
1A776tight positional0.020
4B772tight positional0.020.05
4B772tight positional0.020
4B772tight positional0.020
4B772tight positional0.020
1A641medium positional0.160.5
1A641medium positional0.120
1A641medium positional0.120
1A641medium positional0.130
2A525medium positional0.190.5
2A525medium positional0.190
2A525medium positional0.230
2A525medium positional0.270
3A96medium positional0.110.5
3A96medium positional0.110.01
3A96medium positional0.110
3A96medium positional0.210
4B639medium positional0.140.5
4B639medium positional0.150
4B639medium positional0.150
4B639medium positional0.130
5B333medium positional0.260.5
5B333medium positional0.290
5B333medium positional0.270
5B333medium positional0.240
6B52medium positional0.430.5
6B52medium positional0.550.01
6B52medium positional0.450
6B52medium positional0.450
3A92loose positional0.295
3A92loose positional0.260.05
3A92loose positional0.180
3A92loose positional0.440
6B48loose positional0.45
6B48loose positional0.390.1
6B48loose positional0.530
6B48loose positional0.580
1A776tight thermal0.020.5
1A776tight thermal0.020
1A776tight thermal0.020
1A776tight thermal0.020
4B772tight thermal0.020.5
4B772tight thermal0.010
4B772tight thermal0.020
4B772tight thermal0.020
1A641medium thermal0.022
1A641medium thermal0.020
1A641medium thermal0.020
1A641medium thermal0.020
2A525medium thermal0.112
2A525medium thermal0.130
2A525medium thermal0.140
2A525medium thermal0.120
3A96medium thermal0.072
3A96medium thermal0.090.02
3A96medium thermal0.070
3A96medium thermal0.070
4B639medium thermal0.012
4B639medium thermal0.010
4B639medium thermal0.010
4B639medium thermal0.010
5B333medium thermal0.122
5B333medium thermal0.080.01
5B333medium thermal0.10
5B333medium thermal0.080
6B52medium thermal0.092
6B52medium thermal0.10.04
6B52medium thermal0.050
6B52medium thermal0.080
3A92loose thermal0.0910
3A92loose thermal0.110.11
3A92loose thermal0.10
3A92loose thermal0.070
6B48loose thermal0.1110
6B48loose thermal0.080.21
6B48loose thermal0.080
6B48loose thermal0.070
LS refinement shellResolution: 2.9→2.972 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.401 418 -
Rwork0.35 7656 -
obs--97.99 %

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