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- PDB-3sbx: Crystal structure of a putative uncharacterized protein from Myco... -

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Basic information

Entry
Database: PDB / ID: 3sbx
TitleCrystal structure of a putative uncharacterized protein from Mycobacterium marinum bound to adenosine 5'-monophosphate AMP
ComponentsPutative uncharacterized protein
KeywordsUNKNOWN FUNCTION / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / putative uncharacterized protein / Molybdenum cofactor binding protein / Moco / GTP / orthologs are possible misannotated as possible or putative lysine decarboxylases / AMP was MS verified / proteomics
Function / homology
Function and homology information


: / cytokinin biosynthetic process / hydrolase activity / nucleotide binding
Similarity search - Function
Cytokinin riboside 5'-monophosphate phosphoribohydrolase LOG / LOG family / Possible lysine decarboxylase / Rossmann fold - #450 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / Cytokinin riboside 5'-monophosphate phosphoribohydrolase
Similarity search - Component
Biological speciesMycobacterium marinum M (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Tuberculosis (Edinb) / Year: 2015
Title: Increasing the structural coverage of tuberculosis drug targets.
Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / ...Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / Gardberg, A.S. / Choi, R. / Hewitt, S.N. / Napuli, A.J. / Myers, J. / Barrett, L.K. / Zhang, Y. / Ferrell, M. / Mundt, E. / Thompkins, K. / Tran, N. / Lyons-Abbott, S. / Abramov, A. / Sekar, A. / Serbzhinskiy, D. / Lorimer, D. / Buchko, G.W. / Stacy, R. / Stewart, L.J. / Edwards, T.E. / Van Voorhis, W.C. / Myler, P.J.
History
DepositionJun 6, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 22, 2015Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif / 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_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: Putative uncharacterized protein
B: Putative uncharacterized protein
C: Putative uncharacterized protein
D: Putative uncharacterized protein
E: Putative uncharacterized protein
F: Putative uncharacterized protein
G: Putative uncharacterized protein
H: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,06416
Polymers161,2868
Non-polymers2,7788
Water3,207178
1
A: Putative uncharacterized protein
B: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0164
Polymers40,3222
Non-polymers6942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4950 Å2
ΔGint-27 kcal/mol
Surface area12930 Å2
MethodPISA
2
C: Putative uncharacterized protein
D: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0164
Polymers40,3222
Non-polymers6942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4920 Å2
ΔGint-28 kcal/mol
Surface area13000 Å2
MethodPISA
3
E: Putative uncharacterized protein
F: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0164
Polymers40,3222
Non-polymers6942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4830 Å2
ΔGint-28 kcal/mol
Surface area12890 Å2
MethodPISA
4
G: Putative uncharacterized protein
H: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0164
Polymers40,3222
Non-polymers6942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4850 Å2
ΔGint-28 kcal/mol
Surface area12840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.240, 80.120, 85.690
Angle α, β, γ (deg.)106.70, 90.13, 98.81
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: TRP / Beg label comp-ID: TRP / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: 5 / Auth seq-ID: 11 - 186 / Label seq-ID: 14 - 189

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF
7GG
8HH

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Components

#1: Protein
Putative uncharacterized protein


Mass: 20160.760 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium marinum M (bacteria) / Strain: ATCC BAA-535 / M / Gene: MMAR_4233 / Plasmid: pAVA0421 / Production host: Escherichia coli (E. coli) / References: UniProt: B2HS63
#2: Chemical
ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 2.71 Å3/Da / Density % sol: 54.54 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: MymaA.00620.b.A1 PW29922 at 27.2 mg/mL against JCSG+ screen condition C1, 0.2 M NaCl, 0.1 M phosphate/citrate pH 4.2, 20% PEG 8000 with 25% ethylene glycol as cryo-protection reagent, ...Details: MymaA.00620.b.A1 PW29922 at 27.2 mg/mL against JCSG+ screen condition C1, 0.2 M NaCl, 0.1 M phosphate/citrate pH 4.2, 20% PEG 8000 with 25% ethylene glycol as cryo-protection reagent, crystal tracking ID 218867c1, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 10, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 58548 / Num. obs: 52931 / % possible obs: 90.4 % / Observed criterion σ(I): -3 / Redundancy: 1.8 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 11.16
Reflection shell
Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.5-2.561.70.342.2194.8
2.56-2.640.3312.41194.2
2.64-2.710.2453.36189.1
2.71-2.80.2143.68193.6
2.8-2.890.1874.24193
2.89-2.990.1335.42193.2
2.99-3.10.1136.58192.7
3.1-3.230.0848.27192
3.23-3.370.0729.6190.4
3.37-3.540.05513.21184.8
3.54-3.730.04515.72182.1
3.73-3.950.03718.37182.6
3.95-4.230.03319.81190.1
4.23-4.560.02922.32189.8
4.56-50.02623.79190.3
5-5.590.02921.38190.7
5.59-6.460.03320.98189.6
6.46-7.910.02325.27189.4
7.91-11.180.01835.22187.5
11.180.01538.75185.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 47.43 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å46.36 Å
Translation2.5 Å46.36 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3QUA
Resolution: 2.5→50 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.87 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 25.291 / SU ML: 0.26 / SU R Cruickshank DPI: 0.7924 / Cross valid method: THROUGHOUT / ESU R: 0.793 / ESU R Free: 0.351 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28752 2622 5 %RANDOM
Rwork0.24249 ---
obs0.24468 50303 90.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.994 Å2
Baniso -1Baniso -2Baniso -3
1--1.49 Å2-1.5 Å2-1.07 Å2
2--1.43 Å2-0.76 Å2
3----0.83 Å2
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10435 0 184 178 10797
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02110934
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2531.94815032
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.20451414
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.38123.382411
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.529151478
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5711556
X-RAY DIFFRACTIONr_chiral_restr0.0790.21732
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0218270
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.4951.56985
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.923211040
X-RAY DIFFRACTIONr_scbond_it0.99833949
X-RAY DIFFRACTIONr_scangle_it1.6824.53989
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A702MEDIUM POSITIONAL0.370.5
2B702MEDIUM POSITIONAL0.240.5
3C702MEDIUM POSITIONAL0.230.5
4D702MEDIUM POSITIONAL0.270.5
5E702MEDIUM POSITIONAL0.260.5
6F702MEDIUM POSITIONAL0.250.5
7G702MEDIUM POSITIONAL0.360.5
8H702MEDIUM POSITIONAL0.250.5
1A510LOOSE POSITIONAL0.795
2B510LOOSE POSITIONAL0.525
3C510LOOSE POSITIONAL0.535
4D510LOOSE POSITIONAL0.655
5E510LOOSE POSITIONAL0.465
6F510LOOSE POSITIONAL0.515
7G510LOOSE POSITIONAL0.775
8H510LOOSE POSITIONAL0.55
1A702MEDIUM THERMAL0.532
2B702MEDIUM THERMAL0.362
3C702MEDIUM THERMAL0.62
4D702MEDIUM THERMAL0.412
5E702MEDIUM THERMAL0.822
6F702MEDIUM THERMAL0.562
7G702MEDIUM THERMAL0.562
8H702MEDIUM THERMAL0.372
1A510LOOSE THERMAL0.5710
2B510LOOSE THERMAL0.4710
3C510LOOSE THERMAL0.6210
4D510LOOSE THERMAL0.5210
5E510LOOSE THERMAL0.8610
6F510LOOSE THERMAL0.6810
7G510LOOSE THERMAL0.6610
8H510LOOSE THERMAL0.4510
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 189 -
Rwork0.301 3902 -
obs--94.87 %
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)
12.5331-0.9441.65450.4945-0.39931.4185-0.0989-0.17860.06550.01060.00760.0219-0.0734-0.21530.09130.1077-0.0394-0.0240.1746-0.00510.08235.38182.135920.3327
20.9120.477-0.09222.91730.21260.4711-0.030.0629-0.2125-0.0556-0.0093-0.0722-0.0559-0.15160.03930.0439-0.03-0.00590.2014-0.01530.054411.2926-12.416111.2727
31.27311.23270.04221.26420.22691.54110.0853-0.02610.09360.0195-0.02910.1526-0.0450.1356-0.05610.09970.0491-0.07610.0896-0.04720.1102-7.7845-17.6559-6.4932
40.6729-0.09841.21850.16790.27223.6796-0.1089-0.1854-0.04110.06370.02550.0733-0.1296-0.15780.08330.096-0.05370.01960.2301-0.04750.1051-8.0118-19.479910.6422
52.1063-0.1047-0.08572.04751.03811.5824-0.1796-0.3899-0.30080.23690.0536-0.03570.39940.08290.1260.28320.0779-0.01180.15180.08090.1263-12.3102-11.446456.0924
61.0279-1.0584-0.72621.8895-0.52672.6343-0.1159-0.13640.11540.02060.1588-0.08260.18510.0031-0.04290.0864-0.003-0.08630.1138-0.05910.1332-15.18514.565249.2047
71.68610.18320.73341.4922-0.7091.7476-0.18890.04990.1387-0.12170.0925-0.0201-0.1799-0.13450.09630.0781-0.0253-0.03120.1633-0.03630.0474-33.3052.693430.0154
82.1496-0.55080.71660.60280.21320.59030.08460.0855-0.046-0.02240.0076-0.10450.05920.0585-0.09220.1403-0.01350.05310.1032-0.03230.118-17.0495-4.400530.7298
94.0221.7901-1.20083.18461.36571.92320.0144-0.8713-0.17430.1551-0.54370.3690.06950.15940.52920.15850.0141-0.07830.42530.08690.2224-42.5527-36.27783.7429
101.96880.2471-0.88240.6899-0.21043.5098-0.1204-0.3661-0.3557-0.1274-0.17740.04560.28280.16330.29770.1533-0.01580.150.1571-0.01360.2449-40.3942-45.6098-11.1149
111.59190.5863-0.4991.36690.972.1363-0.15450.17120.0867-0.09570.0770.04610.1338-0.15130.07750.0703-0.0149-0.03520.10490.01090.0802-21.4243-33.0989-25.3202
123.1605-0.0088-0.72650.5680.39170.4372-0.09690.20760.305-0.0035-0.03810.29290.007-0.09290.1350.09010.0325-0.05830.21740.01490.2133-37.8945-27.7869-21.2398
131.1239-0.3977-0.95020.9428-0.44551.5707-0.0204-0.15730.0316-0.0091-0.0173-0.09920.04450.20880.03780.0829-0.0158-0.05330.09350.00220.09596.556-51.842248.6964
140.80440.91690.21531.96880.03020.1703-0.0450.04410.0917-0.0462-0.0210.0397-0.09450.07630.0660.1292-0.0354-0.03660.08030.0410.08950.942-35.393148.9775
151.43511.50150.49071.9065-0.0531.72590.07140.0686-0.01720.03010.0308-0.09920.082-0.0579-0.10220.1371-0.05660.05220.10030.020.141620.1032-20.702537.3523
160.91431.1912-1.4911.6122-2.05642.6792-0.0145-0.1051-0.1504-0.0445-0.068-0.14610.1270.02130.08250.1193-0.0783-0.0810.14050.05270.210820.2245-28.765252.8385
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 99
2X-RAY DIFFRACTION2A100 - 186
3X-RAY DIFFRACTION3B10 - 99
4X-RAY DIFFRACTION4B100 - 186
5X-RAY DIFFRACTION5C10 - 99
6X-RAY DIFFRACTION6C100 - 186
7X-RAY DIFFRACTION7D10 - 99
8X-RAY DIFFRACTION8D100 - 186
9X-RAY DIFFRACTION9E10 - 99
10X-RAY DIFFRACTION10E100 - 186
11X-RAY DIFFRACTION11F10 - 99
12X-RAY DIFFRACTION12F100 - 186
13X-RAY DIFFRACTION13G10 - 99
14X-RAY DIFFRACTION14G100 - 186
15X-RAY DIFFRACTION15H10 - 99
16X-RAY DIFFRACTION16H100 - 186

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