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- PDB-5vu3: Crystal structure of the competence-damaged protein (CinA) superf... -

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Basic information

Entry
Database: PDB / ID: 5vu3
TitleCrystal structure of the competence-damaged protein (CinA) superfamily protein ECL_02051 from Enterobacter cloacae
ComponentsCompetence damage-inducible protein A
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / OUTER MEMBRANE BIOGENESIS / CSGID / NIAID / NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASE / Center for Structural Genomics of Infectious Diseases
Function / homology
Function and homology information


CinA-like / CinA, C-terminal / CinA-like, C-terminal / : / Competence-damaged protein / Maf protein / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Competence damage-inducible protein A
Similarity search - Component
Biological speciesEnterobacter cloacae subsp. cloacae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.868 Å
AuthorsStogios, P.J. / Skarina, T. / McChesney, C. / Sandoval, J. / Di Leo, R. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201200026C United States
CitationJournal: To Be Published
Title: Crystal structure of the competence-damaged protein (CinA) superfamily protein ECL_02051 from Enterobacter cloacae
Authors: Stogios, P.J.
History
DepositionMay 18, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Competence damage-inducible protein A
B: Competence damage-inducible protein A
C: Competence damage-inducible protein A
D: Competence damage-inducible protein A
E: Competence damage-inducible protein A
F: Competence damage-inducible protein A
G: Competence damage-inducible protein A
H: Competence damage-inducible protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,70110
Polymers142,4488
Non-polymers2532
Water32,0491779
1
A: Competence damage-inducible protein A
C: Competence damage-inducible protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6713
Polymers35,6122
Non-polymers591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1870 Å2
ΔGint-10 kcal/mol
Surface area16060 Å2
MethodPISA
2
B: Competence damage-inducible protein A
D: Competence damage-inducible protein A


Theoretical massNumber of molelcules
Total (without water)35,6122
Polymers35,6122
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-10 kcal/mol
Surface area16680 Å2
MethodPISA
3
E: Competence damage-inducible protein A
G: Competence damage-inducible protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8063
Polymers35,6122
Non-polymers1941
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2250 Å2
ΔGint-6 kcal/mol
Surface area15870 Å2
MethodPISA
4
F: Competence damage-inducible protein A
H: Competence damage-inducible protein A


Theoretical massNumber of molelcules
Total (without water)35,6122
Polymers35,6122
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-10 kcal/mol
Surface area15750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.529, 52.825, 132.156
Angle α, β, γ (deg.)85.27, 87.19, 68.98
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Competence damage-inducible protein A


Mass: 17805.939 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter cloacae subsp. cloacae (strain ATCC 13047 / DSM 30054 / NBRC 13535 / NCDC 279-56) (bacteria)
Strain: ATCC 13047 / DSM 30054 / NBRC 13535 / NCDC 279-56 / Gene: cinA, ECL_02051 / Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H3CM13
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1779 / 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: 2.03 Å3/Da / Density % sol: 39.52 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5
Details: PEG 2K MME, 0.2 M ammonium sulfate, 0.1 M sodium acetate pH 4.6, 10 mM nicotinamide mononucleotide

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.87→30 Å / Num. obs: 96710 / % possible obs: 93 % / Redundancy: 2.7 % / Rpim(I) all: 0.04 / Rsym value: 0.053 / Net I/σ(I): 26.33
Reflection shellResolution: 1.87→1.9 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 2.63 / Num. unique obs: 4175 / CC1/2: 0.668 / Rpim(I) all: 0.379 / Rsym value: 0.486 / % possible all: 90.4

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Processing

Software
NameVersionClassification
PHENIX(dev_2733)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5kvk
Resolution: 1.868→29.867 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 20.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1928 1999 2.29 %RANDOM
Rwork0.1512 ---
obs0.1521 87363 94.03 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.868→29.867 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9866 0 17 1779 11662
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00410182
X-RAY DIFFRACTIONf_angle_d0.69713863
X-RAY DIFFRACTIONf_dihedral_angle_d20.9513652
X-RAY DIFFRACTIONf_chiral_restr0.0471700
X-RAY DIFFRACTIONf_plane_restr0.0031786
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8677-1.91440.32721240.26585792X-RAY DIFFRACTION89
1.9144-1.96620.30691420.22415854X-RAY DIFFRACTION91
1.9662-2.0240.23071340.20265999X-RAY DIFFRACTION91
2.024-2.08940.24741470.19395907X-RAY DIFFRACTION92
2.0894-2.1640.25311470.18895974X-RAY DIFFRACTION92
2.164-2.25060.23471320.17216081X-RAY DIFFRACTION93
2.2506-2.3530.23421590.16046069X-RAY DIFFRACTION94
2.353-2.4770.17281460.1596096X-RAY DIFFRACTION94
2.477-2.63210.22191420.16166139X-RAY DIFFRACTION94
2.6321-2.83520.20581330.1616166X-RAY DIFFRACTION96
2.8352-3.12030.17621480.14616254X-RAY DIFFRACTION96
3.1203-3.57110.18451470.13286290X-RAY DIFFRACTION97
3.5711-4.49680.15421450.11416357X-RAY DIFFRACTION98
4.4968-29.87030.15081530.13786386X-RAY DIFFRACTION98
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)
15.13252.555-3.13535.6935-3.69573.512-0.2218-0.2098-0.24830.1967-0.056-0.12320.44090.08230.11440.21580.02810.00950.1757-0.00580.197913.0858-42.866243.3256
28.636-4.0445-2.29715.39925.13867.8442-0.4141-0.1862-0.7244-0.0693-0.0786-0.48870.53760.73450.49050.19290.02260.0570.1970.08590.427.4658-39.475625.4686
36.5431-0.92850.36114.4386-0.50593.9778-0.1557-0.10790.07180.10.06-0.22950.01010.13260.09480.1409-0.04010.02720.09940.01520.174418.7238-29.410722.3845
46.2756-0.34611.3072.286-0.99632.6511-0.10140.3471-0.0395-0.37650.1166-0.08830.058-0.0216-0.02490.2222-0.07050.0510.1433-0.02730.154611.0959-34.73128.3028
53.5056-0.3496-1.32842.56860.41122.9516-0.0530.2218-0.199-0.1931-0.01230.02610.0954-0.39960.06020.1678-0.0670.01870.16060.00710.17625.2093-37.124421.047
61.52791.1416-2.97536.51742.49639.71170.2013-0.9374-1.7942-0.2541-0.0713-1.68981.43460.71530.0520.33890.02410.0620.21310.13810.671520.2665-46.869325.8258
73.76292.7532.90556.09024.75673.995-0.06420.1234-0.12470.3901-0.06010.10661.0744-0.08060.14050.2439-0.01480.02060.22910.03190.25012.2247-45.545122.8833
86.2805-0.0768-4.85611.9954-0.38055.4007-0.16120.3969-0.1266-0.02110.03560.42460.0513-1.03610.130.12140.0188-0.00340.32-0.00560.2275-8.6526-32.538843.03
95.5477-0.2592-0.07665.19970.28264.2796-0.17930.13710.1928-0.05070.09620.1552-0.252-0.31490.07050.11820.0210.00830.143-0.00030.132-0.3173-25.546348.7366
102.46170.9964-2.39472.40442.08917.08660.0086-1.0496-0.43520.4023-0.0189-0.3407-0.2960.3911-0.02840.30030.0203-0.05770.34970.00790.23069.655-26.024865.0575
116.3019-1.79133.87752.7507-1.24075.1631-0.1977-0.2958-0.02270.34910.15-0.05150.049-0.19390.03940.23540.02390.01040.2190.01040.133.6709-34.488963.2932
122.0157-0.7406-0.78752.27790.24283.6159-0.1331-0.2636-0.01220.07930.0644-0.13980.27750.28280.04870.10970.02930.00180.17040.01050.15078.2566-37.376550.4514
133.1262-1.9919-0.1259.01296.27124.96380.2756-0.63881.25060.71610.3203-0.4809-2.2515-0.7269-0.5990.77710.16090.12970.4030.00420.47193.31981.404240.7524
142.26330.26942.40511.65810.16582.65830.05360.15890.16610.0370.0060.255-0.2602-0.7407-0.03880.18670.03670.03010.29040.02370.29383.4217-9.037220.991
153.8215-0.348-0.25314.6609-1.5365.8638-0.068-0.0761-0.09930.13710.10910.2211-0.1029-0.271-0.00630.1036-0.02180.02820.09130.00610.194412.912-18.399120.2957
164.7001-0.81150.6445.0821-0.24653.1227-0.1835-0.2163-0.5802-0.07690.11630.18830.0104-0.09880.10310.1635-0.053-0.00270.11890.01960.168817.1965-21.655714.3576
175.11272.18221.58092.59940.52121.5961-0.12520.2330.2127-0.1616-0.0397-0.3569-0.02910.31650.14230.143-0.04470.03860.19590.05180.249626.7118-13.765510.7127
181.05480.7906-0.49592.52210.43765.00410.0854-0.0410.0030.2226-0.0757-0.2036-0.08390.3961-0.00090.1225-0.04250.00450.14310.01080.210821.2173-10.262323.2937
198.29744.6623-5.9236.3798-5.49357.79390.0120.16590.4278-0.3828-0.0749-0.5019-0.43540.3122-0.01390.3726-0.10270.0180.20120.0260.351725.0126-4.967330.6944
207.21470.53530.0243.43981.0043.9404-0.0498-0.22840.19110.21960.0066-0.3764-0.29360.37080.03790.2007-0.0265-0.02980.11970.02070.193914.4949-14.49451.543
214.86581.12570.23434.1162-1.02444.50420.074-0.107-0.3330.191-0.0388-0.0778-0.34510.0364-0.02690.21560.0452-0.05130.1166-0.02790.14775.3905-18.404955.7594
227.375-4.69072.03035.856-1.72120.6381-0.3011-0.62950.40640.4620.33540.1219-0.373-0.2096-0.01390.39130.10370.0120.2662-0.06040.2523-3.1511-7.065959.5333
232.7096-0.46971.38312.0177-0.31762.7102-0.1582-0.15990.26770.22710.0304-0.1049-0.372-0.18570.1290.27360.0296-0.00150.1358-0.00390.20462.7755-7.28147.3536
245.40515.06046.28395.61736.44217.6653-0.54560.12731.31590.89910.0766-0.2998-1.45470.59010.29040.8232-0.1745-0.2130.33060.02410.493619.2132-2.262351.4549
255.4022-6.19831.6587.8708-0.25264.20360.83170.58271.5165-1.98540.3599-1.3046-1.38031.3808-1.03551.4865-0.46710.19330.8363-0.09860.738730.3304-22.8522-47.612
267.5634-0.34913.2082.14220.38614.3435-0.23940.5045-0.0607-0.35450.2662-0.60180.13831.34090.08810.25050.0080.09780.4632-0.05710.291737.4605-33.4981-25.6599
273.58650.4376-1.82233.20280.94536.714-0.0668-0.0776-0.08440.05060.135-0.08970.48440.4932-0.03890.23510.0162-0.01640.1735-0.01330.16927.6442-37.0897-14.658
282.5157-1.4137-1.38553.3171.21423.57240.0818-0.08240.12910.11640.0676-0.1231-0.07280.2272-0.16770.2032-0.0680.01270.2154-0.02850.18326.5202-26.6882-6.8499
293.142-0.34471.70063.12960.95954.3762-0.10960.02240.068-0.13440.10910.0732-0.39310.02950.00010.2625-0.0080.04960.15680.01760.157922.4198-24.3169-18.3461
303.1912-0.65341.90043.05811.6562.56370.5540.99021.3016-0.69470.3099-1.7502-1.80522.4817-0.74770.4859-0.16680.15810.7711-0.0570.547638.8396-23.9314-23.795
314.55630.88026.27732.34920.71458.73920.0464-1.03320.06870.9806-0.2967-0.2055-2.0303-0.20640.26080.97890.01220.10580.52560.00830.341630.5499-3.5569118.9003
324.44885.35374.32138.29456.43944.9626-0.13020.09350.1705-0.6333-0.07320.1227-0.58130.10030.23170.50820.0330.00690.2559-0.00090.216221.5243-14.5009100.3266
334.8794-2.77571.42726.33150.38493.3833-0.2122-0.33540.1659-0.253-0.14160.6684-0.6189-0.60860.28140.39280.0855-0.09890.3138-0.09530.276613.2799-23.835889.686
347.4030.7195-2.63452.5493-0.01735.34910.03570.6534-0.0142-0.87970.068-0.1856-0.58250.5137-0.10710.54460.0155-0.02230.4255-0.03490.226122.7421-30.931173.437
353.9210.47130.33542.80520.37393.5493-0.31330.52030.0276-0.93970.25410.0345-0.60570.72470.02050.6339-0.0691-0.02020.4080.00370.187726.3083-24.44577.7554
364.6646-0.38942.09832.8555-0.80635.3849-0.15280.31470.4894-0.6390.0570.0286-0.81710.37730.14910.4982-0.0712-0.02010.25250.01650.193225.7033-18.85586.6532
378.0458-3.4172.64515.65562.96746.8228-0.4030.8445-0.4037-0.3749-0.2520.83240.93840.02660.55840.6914-0.3002-0.07230.45570.02910.37340.1406-61.8252-32.1396
382.7197-2.2943-2.60222.25932.37052.58250.043-0.3173-0.08030.3809-0.33490.53740.2284-0.23710.31630.456-0.14350.04910.2862-0.02470.30067.3605-48.3557-12.4784
395.5275-1.2869-0.40983.29320.39383.10210.1789-0.04710.06580.2537-0.07920.14750.3075-0.1509-0.08320.3967-0.0537-0.00660.16890.01510.198218.9776-43.2621-13.0164
403.6093-0.0349-0.37282.487-0.00291.03150.1973-0.2623-0.25470.5348-0.06-0.34410.44240.1627-0.12450.62270.034-0.11570.2399-0.00260.250830.1799-51.8848-5.9762
413.1191-1.033-0.39893.49192.73284.30880.16740.0464-0.19550.1080.0801-0.06630.54090.3045-0.23430.56910.0397-0.10.18360.00520.224924.2214-56.9341-16.5502
423.1035-1.71522.15347.57343.91626.3212-0.5183-0.866-0.9041.5305-0.29531.18080.5388-0.60340.61830.8269-0.17140.0950.40.04740.40738.1838-57.3832-9.1025
437.3932-0.8266-2.12773.8702-4.99357.8639-0.4448-0.8615-1.47330.23710.1853-0.82331.35820.09330.27751.03610.1067-0.29970.44410.05610.771230.0142-57.2509112.9844
443.9317-0.17730.73831.36880.27425.39080.31690.1232-0.3510.47770.0337-0.20870.80450.8469-0.22850.55270.1591-0.17860.3604-0.0730.304328.0993-49.573893.8859
455.2538-2.36910.08945.88531.62092.61510.24810.4277-0.1279-0.1390.0167-0.23630.3870.2207-0.20270.31260.0374-0.07070.22150.0010.149121.2936-41.765186.7755
464.33620.3863-0.5015.89680.97965.4841-0.0965-0.07740.1952-0.00520.01720.0882-0.0823-0.04550.09330.27270.0436-0.02840.214-0.01520.100913.9077-38.673781.8795
474.7267-0.3721-0.22242.88431.09944.40440.1550.1818-0.2657-0.0792-0.27280.36430.1692-0.74850.12770.31220.0114-0.08340.3178-0.03730.24857.7284-44.006984.4596
483.9167-1.3486-0.98413.52722.36797.09190.15880.1036-0.1920.1974-0.13990.13120.6758-0.4534-0.02310.3979-0.0686-0.0440.18630.04580.181911.6322-47.289893.873
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:18)
2X-RAY DIFFRACTION2(chain A and resid 19:30)
3X-RAY DIFFRACTION3(chain A and resid 31:62)
4X-RAY DIFFRACTION4(chain A and resid 63:108)
5X-RAY DIFFRACTION5(chain A and resid 109:163)
6X-RAY DIFFRACTION6(chain A and resid 164:169)
7X-RAY DIFFRACTION7(chain B and resid 0:11)
8X-RAY DIFFRACTION8(chain B and resid 12:30)
9X-RAY DIFFRACTION9(chain B and resid 31:62)
10X-RAY DIFFRACTION10(chain B and resid 63:73)
11X-RAY DIFFRACTION11(chain B and resid 74:105)
12X-RAY DIFFRACTION12(chain B and resid 106:169)
13X-RAY DIFFRACTION13(chain C and resid 3:10)
14X-RAY DIFFRACTION14(chain C and resid 11:29)
15X-RAY DIFFRACTION15(chain C and resid 30:49)
16X-RAY DIFFRACTION16(chain C and resid 50:71)
17X-RAY DIFFRACTION17(chain C and resid 72:103)
18X-RAY DIFFRACTION18(chain C and resid 104:168)
19X-RAY DIFFRACTION19(chain D and resid 0:15)
20X-RAY DIFFRACTION20(chain D and resid 16:48)
21X-RAY DIFFRACTION21(chain D and resid 49:71)
22X-RAY DIFFRACTION22(chain D and resid 72:101)
23X-RAY DIFFRACTION23(chain D and resid 102:163)
24X-RAY DIFFRACTION24(chain D and resid 164:169)
25X-RAY DIFFRACTION25(chain E and resid 2:9)
26X-RAY DIFFRACTION26(chain E and resid 10:30)
27X-RAY DIFFRACTION27(chain E and resid 31:70)
28X-RAY DIFFRACTION28(chain E and resid 71:115)
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