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- PDB-4mn6: Crystal structure of truncated PAS domain from S. aureus YycG -

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Basic information

Entry
Database: PDB / ID: 4mn6
TitleCrystal structure of truncated PAS domain from S. aureus YycG
ComponentsSensor protein kinase WalK
KeywordsTRANSFERASE / PAS domain / Histidine kinase
Function / homology
Function and homology information


histidine kinase / phosphorelay sensor kinase activity / ATP binding / metal ion binding / plasma membrane
Similarity search - Function
HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. / HAMP domain / PAS-associated, C-terminal / PAS domain / PAC domain profile. / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain ...HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. / HAMP domain / PAS-associated, C-terminal / PAS domain / PAC domain profile. / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / PAS domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. / Beta-Lactamase / PAS domain / PAS repeat profile. / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / PAS domain / PAS domain superfamily / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Sensor protein kinase WalK
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsShaikh, N. / Hvorup, R. / Winnen, B. / Collins, B.M. / King, G.F.
CitationJournal: To be Published
Title: Crystal structure of PAS domain of S. aureus YycG
Authors: Shaikh, N. / Hvorup, R. / Winnen, B. / Collins, B.M. / King, G.F.
History
DepositionSep 10, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 10, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _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: Sensor protein kinase WalK
B: Sensor protein kinase WalK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2344
Polymers24,1032
Non-polymers1312
Water95553
1
A: Sensor protein kinase WalK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1172
Polymers12,0521
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sensor protein kinase WalK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1172
Polymers12,0521
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.650, 61.150, 95.640
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 Sensor protein kinase WalK /


Mass: 12051.571 Da / Num. of mol.: 2 / Fragment: UNP residues 73-177
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: vicK, walK, yycG / Plasmid: pGEX2T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9RDT3, histidine kinase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.65 Å3/Da / Density % sol: 53.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 100 mM Tris (pH 8.0), 20 mM ZnCl2, 28% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.1→51.5 Å / Num. obs: 15549 / % possible obs: 99.9 % / Observed criterion σ(I): 2.4 / Redundancy: 13.8 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 17.5
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 14.3 % / Rmerge(I) obs: 0.0113 / Mean I/σ(I) obs: 2.4 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 4MN5

4mn5


Resolution: 2.1→47.82 Å / SU ML: 0.28 / σ(F): 1.36 / Phase error: 29.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.278 777 5.01 %
Rwork0.2205 --
obs0.2232 15502 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→47.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1490 0 2 53 1545
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091502
X-RAY DIFFRACTIONf_angle_d1.392017
X-RAY DIFFRACTIONf_dihedral_angle_d15.248553
X-RAY DIFFRACTIONf_chiral_restr0.055246
X-RAY DIFFRACTIONf_plane_restr0.005251
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.23160.31151270.29332393X-RAY DIFFRACTION100
2.2316-2.40390.36031240.2732414X-RAY DIFFRACTION100
2.4039-2.64580.30841410.26832417X-RAY DIFFRACTION100
2.6458-3.02860.36051220.26842447X-RAY DIFFRACTION100
3.0286-3.81540.27181340.23012468X-RAY DIFFRACTION100
3.8154-47.83230.24431290.18392586X-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)
17.51322.0435-0.33698.10171.63488.66920.1858-0.5181-0.53440.6524-0.2555-0.38370.3810.18830.030.2943-0.0753-0.0650.57340.06290.37273.4843-13.4068-8.6146
26.0126-2.2919-5.08566.05573.17745.2827-0.3051-0.25610.68771.4294-0.2101-0.7185-0.0505-0.37480.58980.5792-0.1106-0.18710.6570.05560.7343-6.6244-19.1031-12.9949
30.94961.95511.38895.2510.4166.57-0.73911.4759-0.6703-0.19750.6685-0.4816-0.54040.82880.16070.3649-0.03680.00860.5264-0.13890.34346.7135-14.0144-16.2917
48.4819-0.4883-2.75354.52020.65248.77840.5994-0.08740.19890.5039-0.0822-0.5826-0.1695-0.553-0.57050.5264-0.0272-0.06340.4549-0.16780.6606-11.2857-24.9926-18.3151
57.3627-1.9951-1.6613.90023.5844.92650.2040.50860.6804-1.295-0.88351.0804-0.6146-2.07330.4560.6110.2406-0.0660.96-0.11190.5855-19.3571-23.4107-24.444
66.0399-6.22032.94276.4821-2.21595.7952-0.6792-0.0157-2.1461-0.30910.10571.88593.5753-1.71920.51591.182-0.18770.32970.7341-0.08020.7068-18.1955-37.6744-18.4229
73.5546-1.1823-2.05858.5055.44134.2466-0.8925-0.538-0.24440.3479-0.5252-0.08271.3325-1.08221.00510.4391-0.00110.08240.5051-0.08580.4756-10.342-32.3395-23.8958
80.0697-0.5170.39563.9363-2.98442.2513-0.0421-1.49131.45370.3419-0.77860.92931.58940.51390.62561.13720.32110.04191.6851-0.49161.0679-10.9893-27.4921-0.2098
98.4138-2.4266-5.03275.82672.89583.26960.0682-0.07880.76270.1160.515-0.48330.03770.1745-0.74050.4729-0.0106-0.0150.3427-0.08860.311-7.8184-28.5851-22.4629
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 269 through 328 )
2X-RAY DIFFRACTION2chain 'A' and (resid 329 through 340 )
3X-RAY DIFFRACTION3chain 'A' and (resid 341 through 369 )
4X-RAY DIFFRACTION4chain 'B' and (resid 267 through 284 )
5X-RAY DIFFRACTION5chain 'B' and (resid 285 through 311 )
6X-RAY DIFFRACTION6chain 'B' and (resid 312 through 330 )
7X-RAY DIFFRACTION7chain 'B' and (resid 331 through 350 )
8X-RAY DIFFRACTION8chain 'B' and (resid 351 through 355 )
9X-RAY DIFFRACTION9chain 'B' and (resid 356 through 369 )

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