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- PDB-3cm1: Crystal structure of SsgA-like sporulation-specific cell division... -

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Basic information

Entry
Database: PDB / ID: 3cm1
TitleCrystal structure of SsgA-like sporulation-specific cell division protein (YP_290167.1) from Thermobifida fusca YX-ER1 at 2.60 A resolution
ComponentsSsgA-like sporulation-specific cell division protein
KeywordsCELL CYCLE / YP_290167.1 / SsgA-like sporulation-specific cell division protein / Streptomyces sporulation and cell division protein / SsgA / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


positive regulation of FtsZ-dependent cytokinesis / cell septum / division septum assembly / sporulation resulting in formation of a cellular spore
Similarity search - Function
Sporulation-specific cell division protein SsgB / Sporulation-specific cell division protein SsgB / Sporulation-specific cell division protein SsgB superfamily / Streptomyces sporulation and cell division protein, SsgA / Transcriptional Co-activator pc4; Chain A / Roll / Mainly Beta
Similarity search - Domain/homology
Sporulation-specific cell division protein SsgB
Similarity search - Component
Biological speciesThermobifida fusca (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å
AuthorsJoint Center for Structural Genomics (JCSG) / Chruszcz, M. / Minor, W. / Wang, S.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Structural and functional characterizations of SsgB, a conserved activator of developmental cell division in morphologically complex actinomycetes.
Authors: Xu, Q. / Traag, B.A. / Willemse, J. / McMullan, D. / Miller, M.D. / Elsliger, M.A. / Abdubek, P. / Astakhova, T. / Axelrod, H.L. / Bakolitsa, C. / Carlton, D. / Chen, C. / Chiu, H.J. / ...Authors: Xu, Q. / Traag, B.A. / Willemse, J. / McMullan, D. / Miller, M.D. / Elsliger, M.A. / Abdubek, P. / Astakhova, T. / Axelrod, H.L. / Bakolitsa, C. / Carlton, D. / Chen, C. / Chiu, H.J. / Chruszcz, M. / Clayton, T. / Das, D. / Deller, M.C. / Duan, L. / Ellrott, K. / Ernst, D. / Farr, C.L. / Feuerhelm, J. / Grant, J.C. / Grzechnik, A. / Grzechnik, S.K. / Han, G.W. / Jaroszewski, L. / Jin, K.K. / Klock, H.E. / Knuth, M.W. / Kozbial, P. / Krishna, S.S. / Kumar, A. / Marciano, D. / Minor, W. / Mommaas, A.M. / Morse, A.T. / Nigoghossian, E. / Nopakun, A. / Okach, L. / Oommachen, S. / Paulsen, J. / Puckett, C. / Reyes, R. / Rife, C.L. / Sefcovic, N. / Tien, H.J. / Trame, C.B. / van den Bedem, H. / Wang, S. / Weekes, D. / Hodgson, K.O. / Wooley, J. / Deacon, A.M. / Godzik, A. / Lesley, S.A. / Wilson, I.A. / van Wezel, G.P.
History
DepositionMar 20, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Apr 13, 2022Group: Database references / Structure summary / Category: audit_author / citation_author / database_2
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Feb 1, 2023Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SsgA-like sporulation-specific cell division protein
B: SsgA-like sporulation-specific cell division protein
C: SsgA-like sporulation-specific cell division protein


Theoretical massNumber of molelcules
Total (without water)46,2483
Polymers46,2483
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4530 Å2
ΔGint-19.7 kcal/mol
Surface area18070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.840, 64.840, 130.600
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41A
51B
61C
71A
81B
91C

NCS domain segments:

Ens-ID: 1 / Refine code: 2

Dom-IDComponent-IDBeg label comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERILEAA7 - 408 - 41
21SERILEBB7 - 408 - 41
31SERILECC7 - 408 - 41
42VALILEAA52 - 8953 - 90
52VALILEBB52 - 8953 - 90
62VALILECC52 - 8953 - 90
73SERALAAA93 - 13494 - 135
83ARGALABB99 - 134100 - 135
93SERALACC93 - 13494 - 135

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Components

#1: Protein SsgA-like sporulation-specific cell division protein


Mass: 15415.895 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermobifida fusca (bacteria) / Strain: YX / Gene: YP_290167.1, Tfu_2111 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q47N25
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 2.97 Å3/Da / Density % sol: 58.56 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: NANODROP, 40.0% 1,2-propanediol, 0.1M Acetate pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837, 0.97929, 0.97898
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 13, 2007 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979291
30.978981
ReflectionResolution: 2.6→46.029 Å / Num. obs: 16529 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 79.297 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 15.84
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.6-2.690.7931.859301579198.9
2.69-2.80.5542.764351683199.9
2.8-2.930.3733.964501689199.9
2.93-3.080.2445.762031625199.9
3.08-3.270.1468.661961621199.9
3.27-3.520.08213.9630316461100
3.52-3.880.04920.564931698199.8
3.88-4.430.03128.962551637199.8
4.43-5.570.0263563691683199.9
5.57-46.0290.02736.559341666196.4

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3data extraction
MAR345CCDdata collection
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.6→46.029 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.915 / SU B: 29.904 / SU ML: 0.277 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.513 / ESU R Free: 0.308
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.27 846 5.1 %RANDOM
Rwork0.23 ---
obs0.232 16493 99.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 63.264 Å2
Baniso -1Baniso -2Baniso -3
1-2.08 Å20 Å20 Å2
2--2.08 Å20 Å2
3----4.15 Å2
Refinement stepCycle: LAST / Resolution: 2.6→46.029 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2892 0 0 0 2892
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222952
X-RAY DIFFRACTIONr_bond_other_d0.0020.021905
X-RAY DIFFRACTIONr_angle_refined_deg1.4141.9524023
X-RAY DIFFRACTIONr_angle_other_deg1.01234634
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.675373
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.73823.75128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.16515425
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.951520
X-RAY DIFFRACTIONr_chiral_restr0.0920.2465
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023307
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02590
X-RAY DIFFRACTIONr_nbd_refined0.2060.2537
X-RAY DIFFRACTIONr_nbd_other0.1750.21759
X-RAY DIFFRACTIONr_nbtor_refined0.1790.21396
X-RAY DIFFRACTIONr_nbtor_other0.0870.21620
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.238
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1820.24
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2480.220
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.070.22
X-RAY DIFFRACTIONr_mcbond_it1.39631941
X-RAY DIFFRACTIONr_mcbond_other0.2033765
X-RAY DIFFRACTIONr_mcangle_it2.40853044
X-RAY DIFFRACTIONr_scbond_it4.44681136
X-RAY DIFFRACTIONr_scangle_it6.66711979
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A595TIGHT POSITIONAL0.060.05
2B595TIGHT POSITIONAL0.050.05
3C595TIGHT POSITIONAL0.050.05
1A655MEDIUM POSITIONAL0.350.25
2B655MEDIUM POSITIONAL0.340.25
3C655MEDIUM POSITIONAL0.290.25
1A595TIGHT THERMAL0.090.5
2B595TIGHT THERMAL0.070.5
3C595TIGHT THERMAL0.080.5
1A655MEDIUM THERMAL0.251
2B655MEDIUM THERMAL0.231
3C655MEDIUM THERMAL0.231
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.432 81 -
Rwork0.383 1115 -
all-1196 -
obs--98.52 %
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)
13.3237-0.76081.45733.16210.72924.4989-0.2266-0.33630.01510.45390.0638-0.10490.1261-0.29930.1628-0.2305-0.06290.0873-0.0691-0.0743-0.159124.760220.6761-4.0513
22.20340.60550.90955.78290.2074.35040.1708-0.3358-0.48910.4645-0.04470.51380.64-0.3466-0.12610.263-0.11290.1789-0.0825-0.0230.146718.8947-2.4831-11.6394
33.06420.1860.79715.31860.06363.97220.0310.1665-0.0475-0.3227-0.11350.99230.1933-0.43030.0825-0.1477-0.10140.036-0.0849-0.07390.050112.082317.0616-23.8404
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1372 - 138
2X-RAY DIFFRACTION2BB1 - 1372 - 138
3X-RAY DIFFRACTION3CC1 - 1372 - 138

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