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- PDB-7s5n: Crystal Structure of a Putative uncharacterized protein from Myco... -

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Basic information

Entry
Database: PDB / ID: 7s5n
TitleCrystal Structure of a Putative uncharacterized protein from Mycobacterium marinum
ComponentsMymaA.17060.a
KeywordsUNKNOWN FUNCTION / SSGCID / Mycobacterium marinum / MMAR_1385 / Uncharacterized protein / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homologyNTF2-like domain superfamily / Uncharacterized protein
Function and homology information
Biological speciesMycobacterium marinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of a Putative uncharacterized protein from Mycobacterium marinum
Authors: Abendroth, J. / Dranow, D.M. / Sankaran, B. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionSep 10, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MymaA.17060.a
B: MymaA.17060.a
C: MymaA.17060.a
D: MymaA.17060.a
E: MymaA.17060.a
F: MymaA.17060.a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,66421
Polymers102,1576
Non-polymers1,50715
Water8,989499
1
A: MymaA.17060.a
E: MymaA.17060.a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5557
Polymers34,0522
Non-polymers5025
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-91 kcal/mol
Surface area11500 Å2
MethodPISA
2
B: MymaA.17060.a
D: MymaA.17060.a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5557
Polymers34,0522
Non-polymers5025
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3240 Å2
ΔGint-91 kcal/mol
Surface area11600 Å2
MethodPISA
3
C: MymaA.17060.a
F: MymaA.17060.a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5557
Polymers34,0522
Non-polymers5025
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint-91 kcal/mol
Surface area11120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.690, 87.600, 185.830
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein
MymaA.17060.a


Mass: 17026.168 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium marinum (strain ATCC BAA-535 / M) (bacteria)
Strain: ATCC BAA-535 / M / Gene: MMAR_1385 / Plasmid: MymaA.17060.a.A1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B2HFJ9
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 499 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.07 Å3/Da / Density % sol: 40.5 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Molecular Dimensions/Calibre Morpheus screen D4: 20mM of each 1,6-Hexanediol, 1-Butanol, 1,2-Propanediol, 2-Propanol, 1,4-Butanediol, 1,3-Propanediol, 100mM Imidazole: MES monohydrate (acid) ...Details: Molecular Dimensions/Calibre Morpheus screen D4: 20mM of each 1,6-Hexanediol, 1-Butanol, 1,2-Propanediol, 2-Propanol, 1,4-Butanediol, 1,3-Propanediol, 100mM Imidazole: MES monohydrate (acid) pH 6.5: 25% (V/V) MPD, 25% (w/V) PEG 1000: 25% (w/V) PEG 3350: tray 233139/233138 d4: cryo: 20% EG: puck lwt7-13

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 27, 2012 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 72690 / % possible obs: 99.5 % / Redundancy: 9.584 % / Biso Wilson estimate: 32.194 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.083 / Rrim(I) all: 0.088 / Χ2: 0.96 / Net I/σ(I): 16.73
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.85-1.97.7420.5224.150710.9210.55895.9
1.9-1.959.1450.3776.3552120.9630.499.9
1.95-2.0110.2290.3217.8250410.9770.338100
2.01-2.0710.2330.2529.7849480.9830.266100
2.07-2.1410.2120.20811.7447520.9870.219100
2.14-2.2110.1830.18712.8546120.9890.197100
2.21-2.2910.1140.17213.8944480.990.181100
2.29-2.3910.1230.15415.3642960.9920.16299.9
2.39-2.4910.0080.13616.7641420.9940.143100
2.49-2.629.8930.11918.9239570.9940.12599.9
2.62-2.769.8260.10720.0537640.9950.11399.9
2.76-2.939.630.09222.2435760.9960.09899.9
2.93-3.139.4380.08224.8533610.9970.087100
3.13-3.389.1740.07326.9531560.9970.077100
3.38-3.78.9960.06628.4728960.9970.06999.9
3.7-4.148.9630.06329.3126350.9970.06799.9
4.14-4.788.9770.05630.2923600.9980.059100
4.78-5.858.9510.05429.6620190.9980.057100
5.85-8.279.1340.05329.3215800.9980.056100
8.27-508.6910.04730.188640.9980.0591.1

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.18 dev 4274refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ab initio model from RobaTTA-fold

Resolution: 1.85→19.84 Å / SU ML: 0.1867 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.9225
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2188 1999 2.75 %0
Rwork0.1839 70688 --
obs0.1848 72687 99.65 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.15 Å2
Refinement stepCycle: LAST / Resolution: 1.85→19.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5999 0 84 499 6582
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00646351
X-RAY DIFFRACTIONf_angle_d0.79928680
X-RAY DIFFRACTIONf_chiral_restr0.0577913
X-RAY DIFFRACTIONf_plane_restr0.00851095
X-RAY DIFFRACTIONf_dihedral_angle_d12.65962261
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.90.24161450.21574743X-RAY DIFFRACTION95.77
1.9-1.950.27291260.21455005X-RAY DIFFRACTION99.9
1.95-20.31651230.21175030X-RAY DIFFRACTION100
2-2.070.24061410.19745033X-RAY DIFFRACTION100
2.07-2.140.23141360.18555012X-RAY DIFFRACTION99.96
2.14-2.230.2291320.19225017X-RAY DIFFRACTION100
2.23-2.330.22561540.19415005X-RAY DIFFRACTION99.94
2.33-2.450.24731650.19475016X-RAY DIFFRACTION99.88
2.45-2.610.21771310.19365080X-RAY DIFFRACTION99.94
2.61-2.810.26631550.2055016X-RAY DIFFRACTION99.94
2.81-3.090.24761460.19695081X-RAY DIFFRACTION99.94
3.09-3.530.18341450.17235112X-RAY DIFFRACTION99.96
3.53-4.440.20911570.15865157X-RAY DIFFRACTION99.91
4.44-19.840.17961430.17535381X-RAY DIFFRACTION99.91
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)
12.519810100071.21616055355-0.7958625166982.43806746845-0.01229691929692.48444878384-0.07991506116040.3143146936440.0885853576382-0.2029606961690.006628478654450.300870160678-0.0864211034458-0.303436666760.07124872690730.1682188440950.00326432333938-0.06873323321910.195226179243-0.007852794508060.179011887094-7.1063454422647.059050682720.3424769548
21.504372544840.442353986708-0.5848254012873.017813242190.3678068712391.95095568742-0.04094265318170.09572840698180.136544809176-0.03941210916210.0680293602708-0.173291817547-0.1156753690020.116181772922-0.02832152581770.120447160936-0.0171830032271-0.0186159510210.1499439903240.01269724387310.15090148172419.529954893627.185151823730.4675372084
33.73139211553-0.864542919725-0.1860171200921.789590800621.149561164862.79865342561-0.127545620356-0.09905461979990.2811291579180.2249816574180.00324392230513-0.05331243032990.0779654983762-0.05228101198860.1128021313750.3168497384960.0366887132357-0.0835554985760.206286534142-0.01886201460610.1952602254-6.9297397602541.082628531-10.9338294489
40.7640071446190.67505448390.2418089005853.20855668654-0.25609176232.19388700556-0.1259677095970.0290663100045-0.1839302852650.1593601118280.0342392304779-0.04547768109460.1886751295910.07586918373220.07346493267240.1252109309580.006573399647320.03345981746230.1462152960750.01925063994260.18021365233112.98773465466.695023749641.8371991775
51.598219462470.315189336633-0.4629705607443.196010150480.1535273185561.565689815560.130224989319-0.08945150290040.2012632827810.124485770301-0.0908897057705-0.0720553528121-0.276670134960.140544820132-0.0419593647290.223228181652-0.0747732694655-0.01091292703650.1816300991450.01525056160550.1651086995647.6808675736362.879625880231.4203737509
61.72280125376-0.948909622565-1.342641881981.047090510180.1086635713261.89766050528-0.0836884852444-1.0330732020.3065316573730.573514107250.389041890922-0.9159599872860.3887037328411.34181132681-0.07152370419560.5473514674440.293486467464-0.240337772410.896678645531-0.2251711756340.52935870434613.572096559637.50880355290.0321914085006
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Label seq-ID: 1

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-ID
11(chain 'A' and resid 1 through 202)AA - C1 - 202
22(chain 'B' and resid -1 through 203)BD - G-1 - 203
33(chain 'C' and resid 1 through 203)CH - K1 - 203
44(chain 'D' and resid 1 through 202)DL - N1 - 202
55(chain 'E' and resid -1 through 203)EO - R-1 - 203
66(chain 'F' and resid 1 through 202)FS - U1 - 202

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