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- PDB-4omv: Crystal Structure of a Putative Macrophage Growth Locus, subunit ... -

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Basic information

Entry
Database: PDB / ID: 4omv
TitleCrystal Structure of a Putative Macrophage Growth Locus, subunit A From Francisella tularensis SCHU S4
ComponentsMacrophage growth locus, subunit A
KeywordsPROTEIN BINDING / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / putative macrophage growth locus / subunit A / potential drug target / virulence/pathogenesis
Function / homology
Function and homology information


Glutathione S-transferase, N-terminal domain / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Up-down Bundle / 3-Layer(aba) Sandwich ...Glutathione S-transferase, N-terminal domain / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Macrophage growth locus, subunit A
Similarity search - Component
Biological speciesFrancisella tularensis subsp. tularensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.75 Å
AuthorsBrunzelle, J.S. / Wawrzak, Z. / Skarina, T. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: Crystal Structure of a Putative Macrophage Growth Locus, subunit A From Francisella tularensis SCHU S4
Authors: Brunzelle, J.S. / Wawrzak, Z. / Skarina, T. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionJan 27, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Macrophage growth locus, subunit A
B: Macrophage growth locus, subunit A


Theoretical massNumber of molelcules
Total (without water)47,5902
Polymers47,5902
Non-polymers00
Water1,15364
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1780 Å2
ΔGint-9 kcal/mol
Surface area21040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.977, 104.977, 101.659
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Macrophage growth locus, subunit A


Mass: 23794.789 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella tularensis subsp. tularensis (bacteria)
Strain: tularensis SCHU S4 / Gene: FTT_1275, mglA / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 gold magic / References: UniProt: Q5NFG1
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 3.4 Å3/Da / Density % sol: 63.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: NaFormate 4M, Tacsimate 3%, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 20, 2012 / Details: Be Lens
RadiationMonochromator: Single Diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. obs: 16516 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Biso Wilson estimate: 82.1 Å2 / Rmerge(I) obs: 0.075 / Χ2: 1.199 / Net I/σ(I): 12.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.75-2.84.90.7488201.008199.6
2.8-2.854.90.5548300.983198.5
2.85-2.94.90.448121.005198.4
2.9-2.964.80.3768171.067199.4
2.96-3.034.90.3228041.074198.7
3.03-3.14.90.2418291.101198.7
3.1-3.174.90.228161.067198.9
3.17-3.264.80.1758211.064199.5
3.26-3.364.80.1368151.116199.1
3.36-3.464.90.1188221.113198.9
3.46-3.594.80.0958401.049199.2
3.59-3.734.80.0828191.104199.2
3.73-3.94.80.0718321.087199.2
3.9-4.114.80.0648071.124199.3
4.11-4.364.80.0628371.14199.5
4.36-4.74.80.0638271.145199.4
4.7-5.174.80.0618331.281199.5
5.17-5.924.70.078441.694199.5
5.92-7.464.70.0728351.958199.5
7.46-504.30.0498561.901197.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
MOLREPphasing
BUSTER-TNTrefinement
PDB_EXTRACT3.14data extraction
BLU-MAXdata collection
HKL-2000data reduction
HKL-2000data scaling
BUSTER2.10.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3MDK

3mdk


Resolution: 2.75→36.51 Å / Cor.coef. Fo:Fc: 0.9552 / Cor.coef. Fo:Fc free: 0.9354 / SU R Cruickshank DPI: 0.501 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2247 1665 10.1 %RANDOM
Rwork0.1867 ---
obs0.1904 16479 99.27 %-
Displacement parametersBiso max: 209.77 Å2 / Biso mean: 90.57 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1-4.4729 Å20 Å20 Å2
2--4.4729 Å20 Å2
3----8.9457 Å2
Refine analyzeLuzzati coordinate error obs: 0.456 Å
Refinement stepCycle: LAST / Resolution: 2.75→36.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3195 0 0 64 3259
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011578SINUSOIDAL2
X-RAY DIFFRACTIONt_angle_deg1.1187HARMONIC2
X-RAY DIFFRACTIONt_omega_torsion2.63436HARMONIC5
X-RAY DIFFRACTIONt_other_torsion3.323248HARMONIC20
LS refinement shellResolution: 2.75→2.94 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3074 294 9.96 %
Rwork0.2454 2658 -
all0.2517 2952 -
obs--99.27 %
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)
10.93412.40985.95162.47127.056214.3165-0.1272-0.38440.19540.31580.4111-0.5477-0.16940.0512-0.2839-0.40870.103-0.2190.0512-0.21870.321518.960550.156316.7723
21.6678-0.96290.4066-1.6678-4.56485.47020.1195-0.13950.30340.2103-0.261-0.4216-0.22620.23460.1415-0.3177-0.08770.0484-0.1918-0.39840.635517.951856.63748.0518
30.2576-0.53690.52792.5553.55460-0.134-0.106-0.08340.5228-0.1858-0.291-0.21970.29830.3197-0.2510.0478-0.04-0.1434-0.34390.189111.645455.396812.1271
47.23752.03694.1533-0.03014.07543.7136-0.124-0.7411-0.20150.7180.13960.2996-0.20090.3245-0.0156-0.15680.0822-0.03580.039-0.2505-0.038.230950.349418.452
59.1641-0.67957.2054-3.8393-1.12912.6390.0261-0.2852-0.11540.185-0.0715-0.3291-0.24820.31970.0453-0.34350.0081-0.27380.6153-0.40770.799627.396752.119120.884
63.5772-0.69222.159313.5911.36712.13180.1847-1.0331-0.03590.6616-0.0182-1.69190.62480.5043-0.1665-0.42660.0898-0.0355-0.1675-0.2134-0.112614.5743.386711.4952
73.4774-1.2078-0.90485.4673-1.42913.13360.15710.25890.8175-1.141-0.0728-1.2133-0.47150.5636-0.0843-0.0824-0.1080.3793-0.362-0.16310.0613.9955.1952-3.0174
84.4452-2.566510.7203-4.4452-3.00322.7475-0.05260.76570.2291-0.77220.06830.375-0.0456-0.232-0.01570.1917-0.12220.5816-0.1278-0.13540.424214.085163.6473-9.7596
9-0.14780.2783-0.32371.0991-0.33890.56450.15890.16520.3139-0.4574-0.01390.0946-0.0054-0.3172-0.1449-0.0031-0.0476-0.0117-0.4308-0.0926-0.05893.466361.4435-5.6319
10-0.64380.63392.58731.2149-3.33153.01580.0482-0.2802-0.02520.1683-0.08010.23670.1585-0.03570.0320.13840.0524-0.0650.41060.20440.3761-5.083257.15182.7865
114.0245-0.6878-2.47338.6029-0.79623.31280.13820.29741.3438-0.6690.3725-1.1022-0.82380.2505-0.5106-0.253-0.07810.1271-0.4179-0.20190.12758.782665.38021.4649
12-1.4623-3.2777-3.619921.66393.15316.83680.0439-0.44630.65470.5130.255-0.3222-0.6106-0.4971-0.2989-0.3637-0.04510.0889-0.3535-0.29020.12644.878565.917510.2925
13-1.21933.5192.25138.68230.32112.57830.07030.18940.1361-0.3785-0.11210.8093-0.0622-0.63660.0418-0.1091-0.0236-0.03630.17370.0857-0.02591.141934.9888-16.3573
142.161-0.1548-0.41343.1245-1.371711.09670.42580.4921-0.0742-0.5978-0.56410.28280.64680.02320.1383-0.00570.1860.0021-0.1034-0.1072-0.121213.171930.4629-13.1345
153.9403-2.36223.9766-3.6382-3.01080.06930.27940.1709-0.2107-0.3375-0.37080.2680.4965-0.10570.09140.0661-0.0564-0.00470.2799-0.11930.0174.532226.0154-9.2233
164.8277-0.58610.37114.6616-2.698210.17090.04940.5160.4631-0.8588-0.07290.2531-0.0611-0.69370.0235-0.12250.0585-0.0502-0.05180.005-0.13934.92737.5885-17.789
173.266-0.7489-2.61454.1812-8.75094.8281-0.271-0.55690.07730.62070.51020.4836-0.4205-1.457-0.2392-0.17980.02830.00140.0696-0.1638-0.12641.786635.3912-3.4018
182.12321.4179-4.82091.186-1.74610.0005-0.08170.0749-0.0433-0.11660.28030.154-0.0291-0.9817-0.19860.0669-0.17830.01770.3245-0.0641-0.2098-1.699227.28091.6831
194.7263-0.8888-1.73450.0016-1.44091.3510.1365-0.26990.1715-0.1848-0.0492-0.1642-0.2229-0.1601-0.0873-0.1929-0.01510.0256-0.0119-0.1691-0.048813.044733.63834.735
206.5334-1.7105-6.205110.16033.78300.26130.03741.0721-0.41640.1166-1.2623-0.61560.2555-0.3779-0.1956-0.01470.0851-0.1064-0.06490.240130.289633.1189-7.8551
211.2859-1.13222.98160.0644-0.78064.4543-0.1245-0.7148-0.08170.71990.20050.2443-0.1479-0.1874-0.076-0.11840.13590.0143-0.053-0.0733-0.204819.783423.8187.0428
22-4.55092.6275-5.37534.5509-6.16352.4184-0.1018-0.449-0.50010.30810.04890.52330.5836-0.11550.05280.4394-0.0691-0.15230.15260.03890.39685.796719.56587.0476
235.4545-4.1363-0.68614.21683.36893.07370.205-0.4059-0.3297-0.01390.00450.14610.45540.1387-0.2095-0.11020.0345-0.0027-0.18310.0195-0.150520.257319.4443-2.5226
248.299-0.51435.47149.30656.74381.3060.25230.017-0.2547-0.3202-0.24680.55950.4856-0.6891-0.00560.0657-0.0279-0.1121-0.1358-0.11130.1658.896118.1152-11.3935
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|0 - 7}A0 - 7
2X-RAY DIFFRACTION2{A|8 - 12}A8 - 12
3X-RAY DIFFRACTION3{A|13 - 17}A13 - 17
4X-RAY DIFFRACTION4{A|18 - 28}A18 - 28
5X-RAY DIFFRACTION5{A|29 - 41}A29 - 41
6X-RAY DIFFRACTION6{A|42 - 80}A42 - 80
7X-RAY DIFFRACTION7{A|81 - 125}A81 - 125
8X-RAY DIFFRACTION8{A|126 - 130}A126 - 130
9X-RAY DIFFRACTION9{A|131 - 139}A131 - 139
10X-RAY DIFFRACTION10{A|140 - 154}A140 - 154
11X-RAY DIFFRACTION11{A|155 - 183}A155 - 183
12X-RAY DIFFRACTION12{A|184 - 202}A184 - 202
13X-RAY DIFFRACTION13{B|0 - 4}B0 - 4
14X-RAY DIFFRACTION14{B|5 - 15}B5 - 15
15X-RAY DIFFRACTION15{B|16 - 20}B16 - 20
16X-RAY DIFFRACTION16{B|21 - 64}B21 - 64
17X-RAY DIFFRACTION17{B|65 - 76}B65 - 76
18X-RAY DIFFRACTION18{B|77 - 81}B77 - 81
19X-RAY DIFFRACTION19{B|82 - 107}B82 - 107
20X-RAY DIFFRACTION20{B|108 - 130}B108 - 130
21X-RAY DIFFRACTION21{B|131 - 140}B131 - 140
22X-RAY DIFFRACTION22{B|141 - 156}B141 - 156
23X-RAY DIFFRACTION23{B|157 - 191}B157 - 191
24X-RAY DIFFRACTION24{B|192 - 203}B192 - 203

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