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- PDB-6blk: Mycobacterial sensor histidine kinase MprB -

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Basic information

Entry
Database: PDB / ID: 6blk
TitleMycobacterial sensor histidine kinase MprB
ComponentsSignal transduction histidine-protein kinase/phosphatase mprB
KeywordsTRANSFERASE / two-component regulatory system / MprAB / Rv0982 / autophosphorylation / kinase domain
Function / homology
Function and homology information


histidine kinase / phosphorelay sensor kinase activity / membrane => GO:0016020 / hydrolase activity / plasma membrane
Similarity search - Function
HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. / HAMP domain / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain ...HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. / HAMP domain / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Histidine kinase
Similarity search - Component
Biological speciesMycobacterium hassiacum
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.552 Å
AuthorsLi, J. / Korotkova, N. / Korotkov, K.V.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI119022 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30GM110787 United States
CitationJournal: to be published
Title: Mycobacterial sensor histidine kinase MprB
Authors: Li, J. / Korotkova, N. / Korotkov, K.V.
History
DepositionNov 10, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 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
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Signal transduction histidine-protein kinase/phosphatase mprB
D: Signal transduction histidine-protein kinase/phosphatase mprB
A: Signal transduction histidine-protein kinase/phosphatase mprB
B: Signal transduction histidine-protein kinase/phosphatase mprB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,66512
Polymers68,5394
Non-polymers2,1268
Water10,557586
1
C: Signal transduction histidine-protein kinase/phosphatase mprB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6663
Polymers17,1351
Non-polymers5312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
D: Signal transduction histidine-protein kinase/phosphatase mprB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6663
Polymers17,1351
Non-polymers5312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
A: Signal transduction histidine-protein kinase/phosphatase mprB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6663
Polymers17,1351
Non-polymers5312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
B: Signal transduction histidine-protein kinase/phosphatase mprB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6663
Polymers17,1351
Non-polymers5312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.410, 61.630, 67.220
Angle α, β, γ (deg.)102.780, 104.470, 109.080
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Signal transduction histidine-protein kinase/phosphatase mprB


Mass: 17134.650 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: fragment residues 322-476, N-terminal GAM residues are from vector, note that UniProt entry has a mis-annotated start codon - therefore a difference in numbering
Source: (gene. exp.) Mycobacterium hassiacum (strain DSM 44199 / CIP 105218 / JCM 12690 / 3849) (bacteria)
Strain: DSM 44199 / CIP 105218 / JCM 12690 / 3849 / Gene: mprB, C731_3480 / Plasmid: pCDF-NT / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3)
References: UniProt: K5BDW2, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases
#2: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 586 / 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: 2.11 Å3/Da / Density % sol: 41.68 % / Description: PRISM
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1 M IMIDAZOLE PH 8.0, 20% PEG8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Nov 2, 2017 / Details: SI(111)
RadiationMonochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→61.42 Å / Num. obs: 74925 / % possible obs: 92.4 % / Observed criterion σ(I): -3 / Redundancy: 2.725 % / Biso Wilson estimate: 22.575 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.066 / Rrim(I) all: 0.081 / Χ2: 1.035 / Net I/σ(I): 9.22
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.55-1.591.4460.3052.1129340.8560.43149.3
1.59-1.642.1940.2932.9354860.9110.37394.2
1.64-1.682.8630.2583.8754550.9450.31994.9
1.68-1.742.7810.2124.6151920.9560.26295
1.74-1.792.770.1855.1551180.9640.22995.3
1.79-1.862.7590.1496.0949580.9770.18495.6
1.86-1.932.6460.1357.3447660.9730.16894.1
1.93-22.8210.1068.445370.9850.13195.9
2-2.092.8210.0969.5844060.9860.11895.7
2.09-2.22.9380.0810.9842650.990.09896.5
2.2-2.312.8010.08111.4439950.9880.195.4
2.31-2.452.920.06912.5838550.9910.08497.1
2.45-2.622.8960.06213.3436220.9920.07697.5
2.62-2.832.880.05914.4233610.9920.07396.6
2.83-3.12.8690.05315.2631400.9930.06597.4
3.1-3.472.8470.05116.1627720.9930.06297
3.47-4.012.8160.05116.7924810.9930.06397.1
4.01-4.912.8670.04717.3920780.9910.05797.5
4.91-6.942.8550.04717.1516370.9930.05797.3
6.94-61.422.8790.05817.728670.9810.07295.7

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Processing

Software
NameVersionClassification
XSCALEVERSION Jun 1, 2017 BUILT=20170923data scaling
PHENIX1.12rc1_2815refinement
PDB_EXTRACT3.22data extraction
XDSVERSION Jun 1, 2017 BUILT=20170923data reduction
BALBES1.0.0.Nov_16_2011phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3D36

3d36


Resolution: 1.552→61.42 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 0.86 / Phase error: 24.88 / Details: REFINEMENT TARGET : ML
RfactorNum. reflection% reflectionSelection details
Rfree0.221 3792 5.09 %RANDOM SELECTION
Rwork0.1838 ---
obs0.1857 74925 86.22 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 100.87 Å2 / Biso mean: 23.9247 Å2 / Biso min: 6.68 Å2
Refinement stepCycle: final / Resolution: 1.552→61.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4702 0 172 586 5460
Biso mean--16.05 29.56 -
Num. residues----613
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114959
X-RAY DIFFRACTIONf_angle_d1.26783
X-RAY DIFFRACTIONf_chiral_restr0.065746
X-RAY DIFFRACTIONf_plane_restr0.008885
X-RAY DIFFRACTIONf_dihedral_angle_d14.8682985
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5521-1.56970.3148360.290955559111
1.5697-1.58820.2756880.2631688177633
1.5882-1.60760.2611240.24032871299555
1.6076-1.62790.2881890.23673809399874
1.6279-1.64930.26252370.23014700493792
1.6493-1.67190.27132740.23264717499192
1.6719-1.69580.24332720.21814656492892
1.6958-1.72110.27242180.21874697491591
1.7211-1.7480.25972530.20754745499892
1.748-1.77670.24652630.19864634489792
1.7767-1.80730.25932710.20314671494292
1.8073-1.84020.22342560.20264747500392
1.8402-1.87560.26132350.20044690492591
1.8756-1.91390.23262060.20884551475787
1.9139-1.95550.22932260.20264552477889
1.9555-2.0010.22162220.17784845506794
2.001-2.0510.2042160.18674908512494
2.051-2.10650.22332290.18694665489491
2.1065-2.16850.23192940.17864833512795
2.1685-2.23850.23942680.18814819508794
2.2385-2.31850.24972900.18254546483690
2.3185-2.41130.2333110.18734857516896
2.4113-2.5210.2582760.17094867514395
2.521-2.6540.23272950.17814871516695
2.654-2.82020.22332710.17354795506694
2.8202-3.0380.20032230.17624857508095
3.038-3.34370.22232660.17454897516394
3.3437-3.82750.18882680.15914782505094
3.8275-4.82190.17342520.15634835508794
4.8219-61.46850.1962730.19594818509194

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