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- PDB-3rnr: Crystal Structure of Stage II Sporulation E Family Protein from T... -

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Basic information

Entry
Database: PDB / ID: 3rnr
TitleCrystal Structure of Stage II Sporulation E Family Protein from Thermanaerovibrio acidaminovorans
ComponentsStage II sporulation E family protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI-Biology / Midwest Center for Structural Genomics / MCSG / alpha-beta-alpha sandwich / phosphatase / cytosol
Function / homology
Function and homology information


Protein phosphatase 2C / Stage II sporulation protein E (SpoIIE) / Sigma factor PP2C-like phosphatases / PPM-type phosphatase domain / Phosphatase 2c; domain 1 / Serine/threonine phosphatases, family 2C, catalytic domain / PPM-type phosphatase domain profile. / PPM-type phosphatase-like domain / PPM-type phosphatase-like domain superfamily / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / Stage II sporulation E family protein
Similarity search - Component
Biological speciesThermanaerovibrio acidaminovorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsKim, Y. / Li, H. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of Stage II Sporulation E Family Protein from Thermanaerovibrio acidaminovorans
Authors: Kim, Y. / Li, H. / Clancy, S. / Joachimiak, A.
History
DepositionApr 22, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Stage II sporulation E family protein
B: Stage II sporulation E family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,29117
Polymers44,0022
Non-polymers1,28915
Water5,098283
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6430 Å2
ΔGint-10 kcal/mol
Surface area17130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.530, 87.349, 93.364
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Stage II sporulation E family protein


Mass: 22000.910 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermanaerovibrio acidaminovorans (bacteria)
Strain: DSM 6589 / Gene: Taci_1699 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Magic / References: UniProt: D1B7C2
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 283 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.04 Å3/Da / Density % sol: 59.49 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES (NaOH) pH 7.5, 10 % (w/v) PEG8000, 10 % (v/v) ethylene Glycol, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97903 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 18, 2010 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97903 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 37141 / Num. obs: 37141 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.8 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 10
Reflection shellResolution: 2→2.03 Å / Redundancy: 8.9 % / Mean I/σ(I) obs: 5.2 / Rsym value: 0.607 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
SHELXSphasing
MLPHAREphasing
BUCCANEERmodel building
PHENIX(phenix.refine: 1.7_650)refinement
HKL-3000data reduction
HKL-3000data scaling
BUCCANEERphasing
RefinementMethod to determine structure: SAD / Resolution: 2→38.021 Å / SU ML: 0.5 / Isotropic thermal model: mixed / σ(F): 1.34 / Phase error: 17.95 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2022 1827 4.97 %
Rwork0.1692 --
obs0.1708 36788 99.69 %
all-36788 -
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.874 Å2 / ksol: 0.362 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.1442 Å2-0 Å2-0 Å2
2---1.976 Å20 Å2
3----1.1681 Å2
Refinement stepCycle: LAST / Resolution: 2→38.021 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2999 0 84 283 3366
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093240
X-RAY DIFFRACTIONf_angle_d1.2824386
X-RAY DIFFRACTIONf_dihedral_angle_d14.091183
X-RAY DIFFRACTIONf_chiral_restr0.11502
X-RAY DIFFRACTIONf_plane_restr0.007582
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.05410.26211520.20212624X-RAY DIFFRACTION99
2.0541-2.11450.22641400.18972644X-RAY DIFFRACTION99
2.1145-2.18280.21031190.1752660X-RAY DIFFRACTION100
2.1828-2.26080.2091310.16392656X-RAY DIFFRACTION100
2.2608-2.35130.20641350.17262660X-RAY DIFFRACTION100
2.3513-2.45830.18991510.17472644X-RAY DIFFRACTION100
2.4583-2.58790.19661300.17552676X-RAY DIFFRACTION100
2.5879-2.74990.21711390.16722681X-RAY DIFFRACTION100
2.7499-2.96220.20951450.16732684X-RAY DIFFRACTION100
2.9622-3.26010.18721570.15742693X-RAY DIFFRACTION100
3.2601-3.73150.22211520.15352697X-RAY DIFFRACTION100
3.7315-4.70.16741330.15232767X-RAY DIFFRACTION100
4.7-38.02790.21211430.19242875X-RAY DIFFRACTION100
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)
11.90430.41-0.43930.6986-0.47810.8518-0.0650.13-0.1246-0.02860.19110.02770.053-0.03340.0160.1905-0.0322-0.01660.16310.03720.176537.87399.056360.9806
21.3906-0.0351-0.94450.8175-0.46281.05750.0193-0.4308-0.22670.0065-0.0651-0.05980.00110.31310.0250.2607-0.0209-0.01580.33170.05870.254246.55985.5275.4615
30.4304-0.35470.7660.7066-0.78181.2681-0.0123-0.0567-0.0412-0.21740.21950.29990.3683-0.7037-0.13230.2144-0.0737-0.02340.23020.0810.232327.9769-3.715977.0421
42.25850.2104-1.06730.7449-0.64670.990.1949-0.6875-0.01370.2172-0.03070.1299-0.0731-0.0503-0.07570.2833-0.01450.01920.2950.00860.243740.74510.928774.6752
51.33310.2812-0.57830.8621-0.31612.9757-0.3322-0.0127-0.5178-0.4360.45430.16790.88280.01620.06260.4716-0.1094-0.0330.26910.07580.37450.1861-2.138964.0643
61.1187-0.50.73550.3676-0.2110.5987-0.2474-0.1265-0.04210.4115-0.0544-0.27050.37150.4612-0.31470.4539-0.0862-0.36030.55130.05090.226763.12120.866769.4335
70.5824-0.0296-0.70810.4061-0.49821.558-0.3082-0.1675-0.8634-0.55530.1886-0.84111.0949-0.04810.07440.6297-0.091-0.04680.35510.12030.425951.1729-4.002270.6126
81.5035-0.7075-0.6871.3784-0.14060.86420.10930.10350.03920.0325-0.0259-0.1775-0.0696-0.1934-0.00620.1928-0.01530.01910.21410.01090.197953.304113.904752.0041
91.37310.6219-0.98331.0343-0.4751.55960.06840.33730.12050.12380.0780.26160.0015-0.3469-0.08420.20040.00610.00230.28680.03280.276748.091417.671547.3657
101.1921-0.0843-0.29190.40230.69611.8137-0.00080.1495-0.0740.0756-0.0097-0.19020.3407-0.0146-0.00650.2678-0.0033-0.00510.2292-0.00210.25762.07545.450644.6168
114.36451.2764-0.0194.08861.23931.7516-0.3464-0.41420.2623-0.54880.03280.436-0.33880.24660.21240.2257-0.01890.00910.24420.01340.232668.949820.620731.1095
121.7218-0.0485-0.82410.5837-0.10461.30660.16920.440.4955-0.16190.1152-0.0338-0.1246-0.1555-0.12510.28540.03230.03110.26220.02690.307358.424622.432539.0152
132.38870.0746-0.80580.98240.21962.2264-0.0351-0.18890.25310.21720.084-0.06010.04830.2133-0.05050.28690.0048-0.00580.26140.00760.315961.01169.005551.2631
143.9262-2.22561.70643.71880.90332.19190.0121-0.2521-0.67580.7403-0.5406-0.70571.0211.3388-0.11310.52420.1789-0.05350.5870.23930.504363.6994-1.654560.9668
151.3988-0.4959-0.90941.2585-0.88351.98720.2343-0.88040.02660.1604-0.6109-0.52550.10290.67360.10330.2804-0.04090.00050.46160.07550.404867.65778.138355.338
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq -2:77)
2X-RAY DIFFRACTION2chain 'A' and (resseq 78:109)
3X-RAY DIFFRACTION3chain 'A' and (resseq 110:133)
4X-RAY DIFFRACTION4chain 'A' and (resseq 134:155)
5X-RAY DIFFRACTION5chain 'A' and (resseq 156:176)
6X-RAY DIFFRACTION6chain 'A' and (resseq 177:190)
7X-RAY DIFFRACTION7chain 'A' and (resseq 191:208)
8X-RAY DIFFRACTION8chain 'B' and (resseq -2:21)
9X-RAY DIFFRACTION9chain 'B' and (resseq 22:77)
10X-RAY DIFFRACTION10chain 'B' and (resseq 78:109)
11X-RAY DIFFRACTION11chain 'B' and (resseq 110:124)
12X-RAY DIFFRACTION12chain 'B' and (resseq 125:143)
13X-RAY DIFFRACTION13chain 'B' and (resseq 144:173)
14X-RAY DIFFRACTION14chain 'B' and (resseq 174:190)
15X-RAY DIFFRACTION15chain 'B' and (resseq 191:208)

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