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Basic information

Entry
Database: PDB / ID: 3lib
TitleCrystal Structure of the extracellular domain of the putative histidine kinase mmHK1S-Z3
ComponentsHypothetical sensory transduction histidine kinase
KeywordsSIGNALING PROTEIN / PDC fold
Function / homology
Function and homology information


Transferases; Transferring phosphorus-containing groups; Phosphotransferases with a nitrogenous group as acceptor / protein histidine kinase activity / signal transduction / plasma membrane
Similarity search - Function
Signal transduction histidine kinase, subgroup 2, dimerisation and phosphoacceptor domain / Histidine kinase / HAMP domain / Double Cache domain 1 / Cache domain / PAS fold-3 / PAS fold / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. / HAMP domain ...Signal transduction histidine kinase, subgroup 2, dimerisation and phosphoacceptor domain / Histidine kinase / HAMP domain / Double Cache domain 1 / Cache domain / PAS fold-3 / PAS fold / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. / HAMP domain / PAS-associated, C-terminal / PAC domain profile. / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / PAS domain / Histidine kinase domain / Histidine kinase domain profile. / Beta-Lactamase / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / PAS domain / PAS domain superfamily / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Hypothetical sensory transduction histidine kinase
Similarity search - Component
Biological speciesMethanosarcina mazei (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.99 Å
AuthorsZhang, Z. / Hendrickson, W.A.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Structural characterization of the predominant family of histidine kinase sensor domains.
Authors: Zhang, Z. / Hendrickson, W.A.
History
DepositionJan 24, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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.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_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 / _struct_conn.ptnr2_label_seq_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: Hypothetical sensory transduction histidine kinase
B: Hypothetical sensory transduction histidine kinase
C: Hypothetical sensory transduction histidine kinase
D: Hypothetical sensory transduction histidine kinase
E: Hypothetical sensory transduction histidine kinase
F: Hypothetical sensory transduction histidine kinase
G: Hypothetical sensory transduction histidine kinase
H: Hypothetical sensory transduction histidine kinase
I: Hypothetical sensory transduction histidine kinase
J: Hypothetical sensory transduction histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)325,16220
Polymers324,77110
Non-polymers39110
Water88349
1
A: Hypothetical sensory transduction histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5162
Polymers32,4771
Non-polymers391
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hypothetical sensory transduction histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5162
Polymers32,4771
Non-polymers391
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Hypothetical sensory transduction histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5162
Polymers32,4771
Non-polymers391
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Hypothetical sensory transduction histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5162
Polymers32,4771
Non-polymers391
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Hypothetical sensory transduction histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5162
Polymers32,4771
Non-polymers391
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Hypothetical sensory transduction histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5162
Polymers32,4771
Non-polymers391
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Hypothetical sensory transduction histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5162
Polymers32,4771
Non-polymers391
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Hypothetical sensory transduction histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5162
Polymers32,4771
Non-polymers391
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: Hypothetical sensory transduction histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5162
Polymers32,4771
Non-polymers391
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
J: Hypothetical sensory transduction histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5162
Polymers32,4771
Non-polymers391
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
11
A: Hypothetical sensory transduction histidine kinase
B: Hypothetical sensory transduction histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,0324
Polymers64,9542
Non-polymers782
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3180 Å2
ΔGint-14 kcal/mol
Surface area23480 Å2
MethodPISA
12
C: Hypothetical sensory transduction histidine kinase
D: Hypothetical sensory transduction histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,0324
Polymers64,9542
Non-polymers782
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint-11 kcal/mol
Surface area22900 Å2
MethodPISA
13
E: Hypothetical sensory transduction histidine kinase
F: Hypothetical sensory transduction histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,0324
Polymers64,9542
Non-polymers782
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3120 Å2
ΔGint-13 kcal/mol
Surface area23030 Å2
MethodPISA
14
G: Hypothetical sensory transduction histidine kinase
H: Hypothetical sensory transduction histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,0324
Polymers64,9542
Non-polymers782
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3170 Å2
ΔGint-10 kcal/mol
Surface area22690 Å2
MethodPISA
15
I: Hypothetical sensory transduction histidine kinase
J: Hypothetical sensory transduction histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,0324
Polymers64,9542
Non-polymers782
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-12 kcal/mol
Surface area23320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.524, 129.524, 404.729
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein
Hypothetical sensory transduction histidine kinase


Mass: 32477.061 Da / Num. of mol.: 10 / Fragment: extracellular domain (UNP residues 32-312)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina mazei (archaea) / Strain: DSM 3647 / Gene: MM_2965 / Plasmid: pET22b+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8PSW1
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: K
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 3.02 Å3/Da / Density % sol: 59.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.7
Details: 2M Na/K phosphate pH6.7, 0.2M NaCl, vapor diffusion, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.96788 Å
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96788 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 76489 / % possible obs: 99.5 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obs% possible all
3-3.113.90.43199.4
3.11-3.2340.29199.2
3.23-3.384.10.21499.6
3.38-3.564.20.1599.8
3.56-3.784.30.113100
3.78-4.074.40.091100
4.07-4.484.50.074100
4.48-5.134.50.065100
5.13-6.464.50.067100
6.46-504.40.05497.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.99 Å49.05 Å
Translation2.99 Å49.05 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER1.3.1phasing
REFMAC5.5.0066refinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.99→46.72 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.883 / Occupancy max: 1 / Occupancy min: 1 / SU B: 18.138 / SU ML: 0.336 / Cross valid method: THROUGHOUT / ESU R Free: 0.449 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27211 3839 5 %RANDOM
Rwork0.19724 ---
obs0.20095 72588 99.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 74.402 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.99→46.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21117 0 10 49 21176
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02221615
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6981.96129358
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.20952688
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.35825.1161032
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.932153474
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.0021567
X-RAY DIFFRACTIONr_chiral_restr0.1040.23204
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02116697
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7591.513393
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.457221555
X-RAY DIFFRACTIONr_scbond_it1.79138222
X-RAY DIFFRACTIONr_scangle_it3.124.57803
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.993→3.071 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 260 -
Rwork0.276 5168 -
obs--96.04 %

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