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- PDB-2q83: Crystal structure of ytaA (2635576) from Bacillus subtilis at 2.5... -

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Basic information

Entry
Database: PDB / ID: 2q83
TitleCrystal structure of ytaA (2635576) from Bacillus subtilis at 2.50 A resolution
ComponentsYtaA protein
KeywordsTRANSFERASE / 2635576 / ytaA / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


endospore-forming forespore / spore wall / sporulation resulting in formation of a cellular spore
Similarity search - Function
Spore coat protein CotS / Aminoglycoside 3'-phosphotransferase; Chain: A, domain 2 / Aminoglycoside phosphotransferase (APH), C-terminal lobe / Aminoglycoside phosphotransferase / Phosphotransferase enzyme family / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase-like domain superfamily / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE / CITRIC ACID / Unknown ligand / Spore coat protein I
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: Proteins / Year: 2010
Title: Genomics, evolution, and crystal structure of a new family of bacterial spore kinases.
Authors: Scheeff, E.D. / Axelrod, H.L. / Miller, M.D. / Chiu, H.J. / Deacon, A.M. / Wilson, I.A. / Manning, G.
History
DepositionJun 8, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 24, 2012Group: Database references
Revision 1.4Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.5Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.6Jul 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 1.7Jan 25, 2023Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300 BIOMOLECULE: 1,2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 ... BIOMOLECULE: 1,2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A MONOMER AS A SIGNIFICANT OLIGOMERIZATION STATE.
Remark 999 SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE ... SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE FOLLOWED BY THE TARGET SEQUENCE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: YtaA protein
B: YtaA protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,22317
Polymers80,8072
Non-polymers1,41515
Water3,369187
1
A: YtaA protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7955
Polymers40,4041
Non-polymers3914
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: YtaA protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,42812
Polymers40,4041
Non-polymers1,02411
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)172.999, 172.999, 192.574
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B

NCS domain segments:

Ens-ID: 1 / Beg label comp-ID: LEU

Dom-IDComponent-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYS6AA22 - 2911 - 18
21LYS6BB22 - 2911 - 18
32ILE4AA30 - 35719 - 346
42ILE4BB30 - 35719 - 346
DetailsSIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A MONOMER AS A SIGNIFICANT OLIGOMERIZATION STATE.

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein YtaA protein


Mass: 40403.703 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: ytaA, BSU30920 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: O34656

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Non-polymers , 6 types, 202 molecules

#2: Chemical ChemComp-ADN / ADENOSINE / Adenosine


Mass: 267.241 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N5O4
#3: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 2 / Source method: obtained synthetically
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 277 K / Method: vapor diffusion, sitting drop / pH: 5.57
Details: NANODROP, 2.23M Ammonium sulfate, 0.1M Citric acid pH 5.57, 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, 0.97904, 0.97932
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 4, 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
20.979041
30.979321
ReflectionResolution: 2.5→29.961 Å / Num. obs: 59155 / % possible obs: 99.9 % / Redundancy: 10.8 % / Biso Wilson estimate: 50.53 Å2 / Rmerge(I) obs: 0.126 / Rsym value: 0.126 / Net I/σ(I): 4.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.5-2.56110.8640.94731943020.864100
2.56-2.64110.6761.14611841950.676100
2.64-2.71110.5991.24483140870.599100
2.71-2.8110.4631.64347439610.463100
2.8-2.89110.3851.94249838700.385100
2.89-2.99110.3082.44083937160.308100
2.99-3.1110.24733953236090.247100
3.1-3.2310.90.1983.83807934800.198100
3.23-3.3710.90.1494.93648733380.149100
3.37-3.5410.90.1235.63476832020.123100
3.54-3.7310.90.0963.23311130470.096100
3.73-3.9510.80.0854.63130229040.085100
3.95-4.2310.80.0758.52946927370.075100
4.23-4.5610.70.0778.42734325630.077100
4.56-510.60.07782487323510.077100
5-5.5910.50.0718.82279521620.071100
5.59-6.4510.50.0778.42011419220.077100
6.45-7.9110.20.0699.31692716540.069100
7.91-11.189.90.04812.21295913100.048100
11.18-29.968.90.05110.566657450.05194.8

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
MolProbity3beta29model building
SCALAdata scaling
PDB_EXTRACT3data extraction
MAR345CCDdata collection
MOSFLMdata reduction
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.5→29.961 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.934 / SU B: 10.512 / SU ML: 0.119 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.206 / ESU R Free: 0.169
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. 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. 4. ELECTRON DENSITIES CORRESPONDING TO RESIDUES 1-21 AND 53-56 IN THE A SUBUNIT AND RESIDUES 1-21 AND 52-55 IN THE B SUBUNIT WERE DISORDERED. THEREFORE, THESE RESIDUES WERE NOT MODELED. 5. CITRIC ACID AND SULFATE MOLECULES FROM THE CRYSTALLIZATION SOLUTION WERE MODELED INTO THE STRUCTURE. THE OCCUPANCIES OF THE SULFATES WERE REDUCED TO ACCOUNT FOR THE REDUCED SCATTERING. 6. SEVERAL MOLECULES OF ETHYLENE GLYCOL, USED AS A CRYOPROTECTANT, WERE MODELED INTO THE STRUCTURE. 7. ADENOSINE WAS MODELED INTO EACH SUBUNIT. THE POSITIONING OF THIS LIGAND IS BASED ON A SIMILAR POSITIONING OF AN ADENOSINE MOIETY IN RELATED STRUCTURES. 8. AN UNKNOWN LIGAND (UNL) WAS MODELED INTO EACH SUBUNIT. 9. ALA A24 AND ASP A65 ARE IN POOR REGIONS OF ELECTRON DENSITY AND ARE RAMACHANDRAN OUTLIERS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21 2988 5.1 %RANDOM
Rwork0.198 ---
obs0.199 59108 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 40.685 Å2
Baniso -1Baniso -2Baniso -3
1--0.36 Å2-0.18 Å20 Å2
2---0.36 Å20 Å2
3---0.54 Å2
Refinement stepCycle: LAST / Resolution: 2.5→29.961 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5286 0 113 187 5586
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0225549
X-RAY DIFFRACTIONr_bond_other_d0.0030.023761
X-RAY DIFFRACTIONr_angle_refined_deg1.6551.9817521
X-RAY DIFFRACTIONr_angle_other_deg1.18239174
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.1555668
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.80524.634246
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.17115945
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.1251525
X-RAY DIFFRACTIONr_chiral_restr0.0670.2821
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026057
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021094
X-RAY DIFFRACTIONr_nbd_refined0.1780.31105
X-RAY DIFFRACTIONr_nbd_other0.1310.33610
X-RAY DIFFRACTIONr_nbtor_refined0.1730.52656
X-RAY DIFFRACTIONr_nbtor_other0.0830.52491
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.5329
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1010.316
X-RAY DIFFRACTIONr_symmetry_vdw_other0.0920.354
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2060.511
X-RAY DIFFRACTIONr_mcbond_it1.51733469
X-RAY DIFFRACTIONr_mcbond_other0.32131334
X-RAY DIFFRACTIONr_mcangle_it2.55655367
X-RAY DIFFRACTIONr_scbond_it4.35682484
X-RAY DIFFRACTIONr_scangle_it6.54112152
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
4317MEDIUM POSITIONAL0.320.5
53LOOSE POSITIONAL0.715
4317MEDIUM THERMAL0.562
53LOOSE THERMAL1.3210
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 183 -
Rwork0.269 4117 -
obs-4300 100 %
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)
15.1078-0.1691-0.45330.4675-0.30491.090.00170.6714-0.6855-0.2986-0.02210.06370.30970.120.0204-0.0980.0423-0.03980.0206-0.0996-0.14419.95266.22676.501
21.9063-0.8372-0.89081.78270.67850.97290.0536-0.18520.45030.05860.1319-0.2433-0.23970.3706-0.1855-0.2157-0.0497-0.0204-0.0153-0.0647-0.129922.84794.319104.694
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA22 - 5211 - 41
2X-RAY DIFFRACTION1AA57 - 35746 - 346
3X-RAY DIFFRACTION2BB22 - 5111 - 40
4X-RAY DIFFRACTION2BB56 - 35745 - 346

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