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Entry
Database: PDB / ID: 2gjv
TitleCrystal Structure of a Protein of Unknown Function from Salmonella typhimurium
Componentsputative cytoplasmic proteinCytoplasm
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologyPhage tail protein-like / Gp37/putative cytoplasmic protein STM4215 / Gp37 protein / STM4215-like / Phage tail protein-like superfamily / 2-Layer Sandwich / metal ion binding / Alpha Beta / Putative cytoplasmic protein
Function and homology information
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.39 Å
AuthorsMinasov, G. / Shuvalova, L. / Brunzelle, J.S. / Vorontsov, I.I. / Collart, F.R. / Joachimiak, A. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of a Hypothetical Protein from Salmonella typhimurium
Authors: Minasov, G. / Shuvalova, L. / Brunzelle, J.S. / Vorontsov, I.I. / Collart, F.R. / Anderson, W.F.
History
DepositionMar 31, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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

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Assembly

Deposited unit
A: putative cytoplasmic protein
B: putative cytoplasmic protein
C: putative cytoplasmic protein
D: putative cytoplasmic protein
E: putative cytoplasmic protein
F: putative cytoplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,36820
Polymers117,8346
Non-polymers53314
Water10,971609
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12420 Å2
ΔGint-140 kcal/mol
Surface area37110 Å2
MethodPISA
2
A: putative cytoplasmic protein
B: putative cytoplasmic protein
C: putative cytoplasmic protein
D: putative cytoplasmic protein
E: putative cytoplasmic protein
F: putative cytoplasmic protein
hetero molecules

A: putative cytoplasmic protein
B: putative cytoplasmic protein
C: putative cytoplasmic protein
D: putative cytoplasmic protein
E: putative cytoplasmic protein
F: putative cytoplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)236,73540
Polymers235,66912
Non-polymers1,06728
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area31020 Å2
ΔGint-289 kcal/mol
Surface area68200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.137, 76.995, 85.112
Angle α, β, γ (deg.)90.00, 109.25, 90.00
Int Tables number5
Space group name H-MC121
DetailsChain A,B,C,D,E, and F represent the biological assembly, which is hexamer

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Components

#1: Protein
putative cytoplasmic protein / Cytoplasm


Mass: 19639.055 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: NP_463080 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3 / References: UniProt: Q8ZKJ0
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 609 / 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

Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: 0.2 M Calcium Chloride dihydrate, 0.25 Sodium Chloride, 0.01 M TRIS-HCL, 20%w/v PEG3350, pH 8.3, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.00882 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 11, 2006 / Details: Mirrors
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00882 Å / Relative weight: 1
ReflectionResolution: 2.39→30 Å / Num. all: 30366 / Num. obs: 30366 / % possible obs: 94 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 16.3
Reflection shellResolution: 2.39→2.49 Å / Redundancy: 3 % / Rmerge(I) obs: 0.116 / Mean I/σ(I) obs: 9.7 / Num. unique all: 3023 / % possible all: 93.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCdata collection
HKL-2000data scaling
PHENIXphasing
SHARPphasing
RefinementMethod to determine structure: SIRAS / Resolution: 2.39→27.9 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.901 / SU B: 15.018 / SU ML: 0.193 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 1.125 / ESU R Free: 0.304 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24883 1520 5 %RANDOM
Rwork0.16788 ---
obs0.17194 28845 93.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 29.096 Å2
Baniso -1Baniso -2Baniso -3
1--0.69 Å20 Å2-0.09 Å2
2---0.66 Å20 Å2
3---1.3 Å2
Refinement stepCycle: LAST / Resolution: 2.39→27.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6348 0 14 609 6971
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0226450
X-RAY DIFFRACTIONr_angle_refined_deg1.5761.9638784
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.3025810
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.78124.49294
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.527151098
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5051548
X-RAY DIFFRACTIONr_chiral_restr0.10.21056
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024830
X-RAY DIFFRACTIONr_nbd_refined0.1830.32760
X-RAY DIFFRACTIONr_nbtor_refined0.3070.54403
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1920.5835
X-RAY DIFFRACTIONr_metal_ion_refined0.1050.57
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1590.3126
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2690.563
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0570.52
X-RAY DIFFRACTIONr_mcbond_it0.7281.54236
X-RAY DIFFRACTIONr_mcangle_it1.15126642
X-RAY DIFFRACTIONr_scbond_it2.06132510
X-RAY DIFFRACTIONr_scangle_it3.224.52142
LS refinement shellResolution: 2.39→2.454 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 112 -
Rwork0.178 1904 -
obs--85.46 %
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)
15.9204-0.8750.13963.9919-1.68274.99780.2273-0.44110.4297-0.0892-0.08310.1136-0.30770.1172-0.1442-0.1088-0.0078-0.0034-0.1636-0.0892-0.126951.908769.111923.707
28.93891.3599-6.02341.2247-1.47.3590.01440.16830.0287-0.1105-0.0308-0.0489-0.0732-0.03540.0163-0.1415-0.0024-0.0258-0.15030.0079-0.197660.649562.694918.5841
33.60080.5248-0.59981.2214-0.76122.4815-0.00640.02180.0226-0.07960.02520.10090.0257-0.1377-0.0189-0.13960.00420.0005-0.1457-0.038-0.165650.582960.13619.6369
44.0103-1.62160.05514.733-0.18521.22460.0186-0.14490.16450.21340.1039-0.2135-0.02230.027-0.1225-0.1122-0.016-0.0227-0.087-0.0119-0.090484.952367.214724.2316
55.2402-3.5056-5.57045.04884.78889.9687-0.0803-0.0889-0.1696-0.12640.0410.1189-0.05640.06330.0394-0.16650.0012-0.0291-0.15670.0451-0.135283.016356.000519.4354
63.0657-0.8045-1.24221.65760.52752.7433-0.0488-0.00170.0959-0.0297-0.01830.1157-0.0216-0.10230.0671-0.14690.0148-0.0257-0.12770.017-0.140276.250263.598919.9884
73.46420.6759-1.18916.30531.03473.49360.0752-0.091-0.07240.4632-0.0306-0.31090.0898-0.0414-0.0446-0.12260.0227-0.0693-0.0980.0284-0.134298.386139.820727.1975
86.36123.05962.988912.33498.755911.9357-0.17930.6145-0.1265-1.0160.06830.1954-0.3068-0.26260.1109-0.0231-0.0141-0.0026-0.1153-0.0018-0.145486.140726.88119.8179
91.81250.2064-0.09683.05061.16642.5239-0.03220.08030.1327-0.0718-0.0479-0.0014-0.1186-0.01370.0801-0.12540.0054-0.0091-0.16090.0354-0.159992.521543.427520.1668
103.99110.7450.96953.43840.9323.81830.1924-0.4273-0.33760.1305-0.14770.06860.0961-0.0534-0.0446-0.1026-0.02690.0279-0.11110.0582-0.129782.638713.120827.4451
1120.42121.039413.14915.80990.119814.9731-0.0671.3306-0.0909-0.6360.18450.25340.01150.2695-0.1175-0.15840.00570.0139-0.0085-0.0071-0.13465.377316.70979.8422
123.831.10661.19422.1790.44192.731-0.05050.07630.1254-0.0092-0.08960.1067-0.11390.08690.1401-0.1754-0.00060.031-0.14050.0295-0.157682.91219.629720.2396
135.42840.0932.04093.88331.23754.6206-0.2247-0.6359-0.24340.33720.34850.36420.035-0.294-0.1238-0.10120.00240.073-0.04110.0429-0.046751.377612.658227.2706
149.4001-4.18624.88378.9309-5.958812.84460.23710.92570.163-0.7507-0.28530.20420.01920.28080.0482-0.07350.0464-0.0288-0.0808-0.0413-0.051345.920829.9259.4488
153.6847-1.05531.88861.6367-0.72463.3962-0.01460.0204-0.14480.0542-0.00460.11750.01680.06430.0192-0.13280.00740.0276-0.1293-0.0079-0.115257.267115.837220.2308
164.0676-0.28180.92856.3101-1.47653.02950.1101-0.2681-0.21930.865-0.11420.3809-0.11830.01240.0041-0.0098-0.00830.0762-0.1054-0.0224-0.053535.276739.563827.2093
174.16461.5023-2.50397.4954-4.83266.4934-0.01290.3285-0.0791-0.7108-0.1105-0.12160.29940.21080.1234-0.0453-0.027-0.026-0.13580.0015-0.141447.400451.918110.4148
181.57610.3962-0.14615.33-1.77472.8445-0.0563-0.029-0.25850.0922-0.10040.1140.07390.03420.1567-0.1224-0.00080.0318-0.1661-0.0162-0.068541.275635.978120.124
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA-1 - 3123 - 55
2X-RAY DIFFRACTION2AA32 - 6956 - 93
3X-RAY DIFFRACTION3AA70 - 13494 - 158
4X-RAY DIFFRACTION4BB-1 - 3023 - 54
5X-RAY DIFFRACTION5BB31 - 6955 - 93
6X-RAY DIFFRACTION6BB70 - 13494 - 158
7X-RAY DIFFRACTION7CC-1 - 4523 - 69
8X-RAY DIFFRACTION8CC46 - 6870 - 92
9X-RAY DIFFRACTION9CC69 - 13493 - 158
10X-RAY DIFFRACTION10DD-1 - 4523 - 69
11X-RAY DIFFRACTION11DD46 - 6870 - 92
12X-RAY DIFFRACTION12DD69 - 13493 - 158
13X-RAY DIFFRACTION13EE-1 - 4523 - 69
14X-RAY DIFFRACTION14EE46 - 6770 - 91
15X-RAY DIFFRACTION15EE68 - 13492 - 158
16X-RAY DIFFRACTION16FF-1 - 4423 - 68
17X-RAY DIFFRACTION17FF45 - 6869 - 92
18X-RAY DIFFRACTION18FF69 - 13493 - 158

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