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- PDB-6mr3: Crystal structure of the competence-damaged protein (CinA) superf... -

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Basic information

Entry
Database: PDB / ID: 6mr3
TitleCrystal structure of the competence-damaged protein (CinA) superfamily protein from Streptococcus mutans
ComponentsPutative competence-damage inducible protein
KeywordsSTRUCTURAL GENOMICS / ALPHA/BETA PROTEIN / COMPETENCE / DAMAGE / MIDWEST CENTER FOR STRUCTUAL GENOMICS / MCSG / PSI-BIOLOGY / PUTATIVE nicotinamide mononucleotide deamidase / NMN / Midwest Center for Structural Genomics
Function / homology
Function and homology information


Competence-induced protein CinA / CinA, KH domain / Damage-inducible protein CinA KH domain / CinA-like / CinA, C-terminal / CinA-like, C-terminal / Competence-damaged protein / Maf protein / MoaB/Mog domain / MoaB/Mog-like domain superfamily ...Competence-induced protein CinA / CinA, KH domain / Damage-inducible protein CinA KH domain / CinA-like / CinA, C-terminal / CinA-like, C-terminal / Competence-damaged protein / Maf protein / MoaB/Mog domain / MoaB/Mog-like domain superfamily / Probable molybdopterin binding domain / Probable molybdopterin binding domain / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Putative competence-damage inducible protein
Similarity search - Component
Biological speciesStreptococcus mutans serotype c (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.05 Å
AuthorsStogios, P.J. / Cuff, M. / Xu, X. / Cui, H. / Di Leo, R. / Yim, V. / Chin, S. / Savchenko, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM094585 United States
CitationJournal: To Be Published
Title: Crystal structure of the competence-damaged protein (CinA) superfamily protein from Streptococcus mutans
Authors: Stogios, P.J.
History
DepositionOct 11, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Data collection / Structure summary / Category: audit_author
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support
Item: _pdbx_audit_support.country / _pdbx_audit_support.funding_organization
Revision 1.3May 13, 2020Group: Structure summary / Category: audit_author / Item: _audit_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative competence-damage inducible protein
B: Putative competence-damage inducible protein
C: Putative competence-damage inducible protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,3457
Polymers138,2033
Non-polymers1424
Water9,656536
1
A: Putative competence-damage inducible protein
hetero molecules

B: Putative competence-damage inducible protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,2776
Polymers92,1352
Non-polymers1424
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_546-x+1/2,y-1/2,-z+11
Buried area2640 Å2
ΔGint-45 kcal/mol
Surface area21680 Å2
MethodPISA
2
C: Putative competence-damage inducible protein

C: Putative competence-damage inducible protein


Theoretical massNumber of molelcules
Total (without water)92,1352
Polymers92,1352
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_657-x+1,y,-z+21
Buried area2120 Å2
ΔGint-7 kcal/mol
Surface area21720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.030, 54.507, 111.013
Angle α, β, γ (deg.)90.00, 125.38, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Putative competence-damage inducible protein


Mass: 46067.746 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans serotype c (strain ATCC 700610 / UA159) (bacteria)
Strain: ATCC 700610 / UA159 / Gene: cinA, SMU_2086 / Plasmid: p15Tv lic / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL / References: UniProt: Q8DRX2
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 536 / 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: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M bis-tris ph5.5, 0.2M ammonium acetate, 25%PEG3350, papain protease

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97904 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 21, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97904 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 54303 / % possible obs: 99.2 % / Redundancy: 4.7 % / Rsym value: 0.081 / Net I/σ(I): 13.49
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 3.41 / Num. unique obs: 2619 / Rsym value: 0.482 / % possible all: 98.2

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
PHENIXmodel building
DMmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.05→41.212 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 20.82 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2152 1735 3.77 %RANDOM
Rwork0.1857 ---
obs0.1868 45969 98.02 %-
Solvent computationShrinkage radii: 1.1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.05→41.212 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5635 0 4 536 6175
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045730
X-RAY DIFFRACTIONf_angle_d0.7777728
X-RAY DIFFRACTIONf_dihedral_angle_d19.222122
X-RAY DIFFRACTIONf_chiral_restr0.049905
X-RAY DIFFRACTIONf_plane_restr0.005982
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.12330.24471660.21564239X-RAY DIFFRACTION95
2.1233-2.20830.26671670.20574278X-RAY DIFFRACTION96
2.2083-2.30880.23791720.19674359X-RAY DIFFRACTION97
2.3088-2.43050.23991710.19534381X-RAY DIFFRACTION98
2.4305-2.58280.21891740.19874417X-RAY DIFFRACTION98
2.5828-2.78210.2181750.20034459X-RAY DIFFRACTION99
2.7821-3.0620.2291750.19954462X-RAY DIFFRACTION99
3.062-3.50490.23071770.19224502X-RAY DIFFRACTION100
3.5049-4.4150.18471780.16484533X-RAY DIFFRACTION100
4.415-41.22070.19421800.16914604X-RAY DIFFRACTION99
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)
14.25712.40710.54032.53562.54514.398-0.1578-0.2956-0.1360.3583-0.1695-0.70410.50690.90770.25110.2580.0302-0.03340.51520.18250.401642.730516.186975.1605
25.10912.5362-0.71574.0337-0.30673.9197-0.0072-0.77420.06310.2854-0.4401-1.3261-0.38711.26080.37560.3403-0.522-0.19280.69780.36280.940852.647227.275973.8929
30.9631-1.40531.29923.1787-1.25022.1199-0.0367-0.2735-0.93250.1516-0.3538-0.88590.40640.9440.03560.43810.104-0.09970.94040.39350.765547.616215.544676.1448
43.9297-1.33812.81372.1248-2.36355.1893-0.0914-0.5799-0.11220.4691-0.1038-0.3236-0.24980.38670.06850.3111-0.0447-0.05090.40760.07060.242734.043721.845674.8833
52.10970.2295-0.54843.7546-1.57652.38240.0711-0.14080.10880.1431-0.04080.1177-0.1074-0.0688-0.04760.0914-0.005-0.01220.1201-0.02390.118520.882832.364453.2833
63.3046-1.2807-1.82813.665-0.00773.55980.0096-0.06570.19990.1456-0.1272-0.2943-0.11570.02010.02430.1612-0.0497-0.04460.2152-0.00790.236332.718836.529655.2164
77.0615-1.7664-3.58844.84212.45082.84130.0809-0.2740.29890.4424-0.0315-0.107-0.0251-0.3107-0.02350.1619-0.0054-0.05040.2380.030.169430.102929.558864.2418
83.7591.0888-0.92810.3433-0.3093.64740.18680.2913-0.04880.22040.03350.78950.0355-0.5334-0.18290.3104-0.07520.11380.26850.01980.5913-27.946823.086354.7949
93.23020.2889-0.0352.7804-0.9525.41860.4327-0.49070.29610.5655-0.05410.6813-0.1798-0.2631-0.30060.4297-0.13570.19240.3125-0.0970.4668-28.495226.993561.8594
103.43070.3835-1.01682.5012-0.51072.8729-0.0022-0.1305-0.12310.3218-0.04910.35650.0661-0.07610.02660.15250.00230.02220.1203-0.01470.2238-14.670747.040849.5895
114.9075-1.5307-2.79124.0461.41244.4118-0.03310.0661-0.0540.02010.0247-0.1133-0.08120.18310.00180.1105-0.0098-0.06370.13920.00960.19113.359646.245944.6008
125.89653.05583.17738.12993.55834.43790.01350.2619-0.7755-0.03410.3903-0.26170.29810.3307-0.29170.15580.00010.00370.1099-0.03270.315-3.050334.514143.9456
136.1135-0.0875-1.71666.79330.13546.53310.2246-0.5632-0.35820.69760.0299-0.12440.29190.0492-0.29350.1552-0.04620.00790.10330.02060.2537-10.842737.947551.9623
142.45860.58240.31515.27534.73954.4855-0.012-0.0516-0.01830.96920.12680.36211.88730.11870.04841.3340.13210.02220.4632-0.09040.2354-5.3819-27.670578.518
156.57195.54083.34357.82442.30443.78990.0534-0.04530.1142-0.34780.05810.16640.31620.0195-0.10740.60880.1167-0.03690.5849-0.09010.2726-4.4199-18.372673.1729
165.9145-1.7684-0.72224.68021.36634.7981-0.12080.15620.7059-0.0946-0.18180.0763-0.5012-0.18520.26140.40350.0304-0.08440.3163-0.0150.36273.80985.617289.3638
176.8352-0.3982-0.52577.1134-0.75982.7681-0.0882-0.22840.01570.2968-0.0630.7001-0.223-0.30910.15560.28990.02210.00640.3349-0.10360.2909-3.8375-4.248190.4325
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 174 through 187 )
2X-RAY DIFFRACTION2chain 'A' and (resid 188 through 200 )
3X-RAY DIFFRACTION3chain 'A' and (resid 201 through 226 )
4X-RAY DIFFRACTION4chain 'A' and (resid 227 through 279 )
5X-RAY DIFFRACTION5chain 'A' and (resid 280 through 355 )
6X-RAY DIFFRACTION6chain 'A' and (resid 356 through 391 )
7X-RAY DIFFRACTION7chain 'A' and (resid 392 through 418 )
8X-RAY DIFFRACTION8chain 'B' and (resid 174 through 214 )
9X-RAY DIFFRACTION9chain 'B' and (resid 215 through 254 )
10X-RAY DIFFRACTION10chain 'B' and (resid 255 through 308 )
11X-RAY DIFFRACTION11chain 'B' and (resid 309 through 355 )
12X-RAY DIFFRACTION12chain 'B' and (resid 356 through 391 )
13X-RAY DIFFRACTION13chain 'B' and (resid 392 through 418 )
14X-RAY DIFFRACTION14chain 'C' and (resid 174 through 226 )
15X-RAY DIFFRACTION15chain 'C' and (resid 227 through 271 )
16X-RAY DIFFRACTION16chain 'C' and (resid 272 through 355 )
17X-RAY DIFFRACTION17chain 'C' and (resid 356 through 414 )

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