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- PDB-3mf4: Crystal structure of putative two-component system response regul... -

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Basic information

Entry
Database: PDB / ID: 3mf4
TitleCrystal structure of putative two-component system response regulator/ggdef domain protein
ComponentsTwo-component system response regulator/GGDEF domain protein
KeywordsSIGNALING PROTEIN / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / NYSGXRC / TWO-COMPONENT SYSTEM RESPONSE REGULATOR / PSI-2 / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


diguanylate cyclase / phosphorelay signal transduction system / metal ion binding
Similarity search - Function
Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain / Nucleotide cyclase / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily ...Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain / Nucleotide cyclase / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Response regulator / Reverse transcriptase/Diguanylate cyclase domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesAeromonas salmonicida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsMalashkevich, V.N. / Toro, R. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of putative two-component system response regulator/ggdef domain protein
Authors: Malashkevich, V.N. / Toro, R. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionApr 1, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 8, 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 1.3Nov 21, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.pdbx_leaving_atom_flag / _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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 6, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.6Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.7Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Two-component system response regulator/GGDEF domain protein
B: Two-component system response regulator/GGDEF domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,8236
Polymers59,7262
Non-polymers974
Water4,486249
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3450 Å2
ΔGint-46 kcal/mol
Surface area21130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.919, 53.269, 57.908
Angle α, β, γ (deg.)61.950, 81.090, 78.760
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A-99999 - 99999
2111B-99999 - 99999

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Components

#1: Protein Two-component system response regulator/GGDEF domain protein


Mass: 29863.020 Da / Num. of mol.: 2 / Fragment: sequence database residues 2-249
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeromonas salmonicida (bacteria) / Strain: A449 / Gene: ASA_2441 / Plasmid: BC-PSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CODON+RIL / References: UniProt: A4SNL2
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / 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: 1.82 Å3/Da / Density % sol: 32.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20% PEG 8000, 0.1 M Tris, 0.2 M MgCl2, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 29, 2009
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 33709 / % possible obs: 86.2 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.07 / Χ2: 1.496 / Net I/σ(I): 11.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.8-1.831.90.2911801.408158.9
1.83-1.861.90.25912421.417164.3
1.86-1.91.90.22415171.411178.2
1.9-1.941.90.19218621.506193.8
1.94-1.981.90.19218391.551194
1.98-2.0320.15517971.514193.1
2.03-2.0820.14717961.52192.1
2.08-2.1320.12918191.511192
2.13-2.220.11717571.682191.1
2.2-2.2720.10617951.642191
2.27-2.351.90.09817651.648191.6
2.35-2.441.90.09417911.618190.9
2.44-2.551.90.08117831.485190.6
2.55-2.691.90.07717531.552190.2
2.69-2.861.90.07117751.572190.5
2.86-3.081.90.06117471.397189.7
3.08-3.391.90.05717841.36190.7
3.39-3.881.90.04916561.205185.1
3.88-4.881.80.04915461.265178.9
4.88-501.90.05215051.477177.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 36.47 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å27.63 Å
Translation2.5 Å27.63 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3LUF

3luf


Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.872 / WRfactor Rfree: 0.277 / WRfactor Rwork: 0.23 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.801 / SU B: 8.181 / SU ML: 0.116 / SU R Cruickshank DPI: 0.23 / SU Rfree: 0.193 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.23 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.273 1662 5 %RANDOM
Rwork0.222 ---
obs0.224 33220 85.07 %-
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 max: 51.28 Å2 / Biso mean: 12.726 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å2-0.2 Å20.03 Å2
2--0.47 Å2-0.34 Å2
3---0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3898 0 4 249 4151
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0224033
X-RAY DIFFRACTIONr_angle_refined_deg1.2851.9755466
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5155508
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.79823.846195
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.17115753
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4131539
X-RAY DIFFRACTIONr_chiral_restr0.0910.2635
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213022
X-RAY DIFFRACTIONr_mcbond_it1.0493.52492
X-RAY DIFFRACTIONr_mcangle_it3.281504027
X-RAY DIFFRACTIONr_scbond_it7.613501541
X-RAY DIFFRACTIONr_scangle_it1.3034.51435
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1942 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
TIGHT POSITIONAL3.125
TIGHT THERMAL3.3210
LS refinement shellResolution: 1.801→1.848 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 62 -
Rwork0.288 1229 -
all-1291 -
obs--44.46 %
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)
10.22040.1880.4930.5180.6671.3226-0.0051-0.0054-0.0059-0.01130.01270.022-0.0405-0.0118-0.00760.0210.00330.00910.01170.01410.0199-14.381613.6274-22.3931
20.00970.01030.04010.48840.52841.49090.0074-0.0048-0.00990.041-0.01130.03230.1101-0.00960.00390.01330.00170.00350.01070.01730.0354-1.6711-11.55-26.0676
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 246
2X-RAY DIFFRACTION1A300 - 301
3X-RAY DIFFRACTION1A259 - 383
4X-RAY DIFFRACTION2B2 - 247
5X-RAY DIFFRACTION2B300 - 301
6X-RAY DIFFRACTION2B260 - 387

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