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- PDB-3m6m: Crystal structure of RpfF complexed with REC domain of RpfC -

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Basic information

Entry
Database: PDB / ID: 3m6m
TitleCrystal structure of RpfF complexed with REC domain of RpfC
Components
  • RpfF protein
  • Sensory/regulatory protein rpfC
KeywordsLYASE/TRANSFERASE / RpfF / REC / RpfC / enoyl-CoA hydratase / LYASE-TRANSFERASE complex
Function / homology
Function and homology information


fatty acid beta-oxidation / histidine kinase / phosphorelay sensor kinase activity / : / membrane => GO:0016020 / ATP binding / plasma membrane
Similarity search - Function
Light-harvesting Protein - #30 / Light-harvesting Protein / Histidine Phosphotransfer domain / Hpt domain / Histidine-containing phosphotransfer (HPt) domain profile. / Signal transduction histidine kinase, phosphotransfer (Hpt) domain / HPT domain superfamily / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / His Kinase A (phospho-acceptor) domain ...Light-harvesting Protein - #30 / Light-harvesting Protein / Histidine Phosphotransfer domain / Hpt domain / Histidine-containing phosphotransfer (HPt) domain profile. / Signal transduction histidine kinase, phosphotransfer (Hpt) domain / HPT domain superfamily / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Other non-globular / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / ClpP/crotonase-like domain superfamily / Response regulator / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Special / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
IODIDE ION / Sensory/regulatory protein RpfC / RpfF protein
Similarity search - Component
Biological speciesXanthomonas campestris pv. campestris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / ML / Resolution: 2.5 Å
AuthorsCheng, Z. / Lim, S.C. / Qamra, R. / Song, H.
CitationJournal: Structure / Year: 2010
Title: Structural Basis of the Sensor-Synthase Interaction in Autoinduction of the Quorum Sensing Signal DSF Biosynthesis
Authors: Cheng, Z. / He, Y.W. / Lim, S.C. / Qamra, R. / Walsh, M.A. / Zhang, L.H. / Song, H.
History
DepositionMar 16, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 16, 2013Group: Derived calculations
Revision 1.3Mar 20, 2024Group: 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_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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_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.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_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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: RpfF protein
B: RpfF protein
C: RpfF protein
D: Sensory/regulatory protein rpfC
E: Sensory/regulatory protein rpfC
F: Sensory/regulatory protein rpfC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,92926
Polymers147,8946
Non-polymers2,03620
Water543
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)130.913, 130.913, 156.471
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 1 / Auth seq-ID: 14 - 279 / Label seq-ID: 30 - 295

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC

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Components

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Protein , 2 types, 6 molecules ABCDEF

#1: Protein RpfF protein / ENOYL-COA HYDRATASE


Mass: 33568.484 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas campestris pv. campestris (bacteria)
Gene: rpfF, XCC1857 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7CLS3
#2: Protein Sensory/regulatory protein rpfC / Response regulator


Mass: 15729.422 Da / Num. of mol.: 3 / Fragment: UNP residues 400-541
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas campestris pv. campestris (bacteria)
Gene: rpfC, XCC1856 / Production host: Escherichia coli (E. coli) / References: UniProt: P0C0F6, histidine kinase

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Non-polymers , 4 types, 23 molecules

#3: Chemical
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: I
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 3 / 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: 2.62 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100mM MES-Na, 20% PEG 4000, 200mM MgCl2, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 14, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 56289 / % possible obs: 97 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellHighest resolution: 2.5 Å / % possible all: 96

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Phasing

PhasingMethod: ML

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Processing

Software
NameVersionClassificationNB
PHASERphasing
REFMAC5.4.0077refinement
PDB_EXTRACT3.1data extraction
DNAdata collection
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.893 / Occupancy max: 1 / Occupancy min: 1 / SU B: 20.639 / SU ML: 0.218 / Cross valid method: THROUGHOUT / ESU R: 0.487 / ESU R Free: 0.289 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27116 2664 5.1 %RANDOM
Rwork0.25005 ---
obs0.25113 49730 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.271 Å2
Baniso -1Baniso -2Baniso -3
1--2.12 Å2-1.06 Å20 Å2
2---2.12 Å20 Å2
3---3.18 Å2
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8685 0 29 3 8717
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0228815
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9041.96511902
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.96951120
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.4723.443395
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.169151548
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5021584
X-RAY DIFFRACTIONr_chiral_restr0.0570.21382
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0216563
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_it0.251.55597
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.49128926
X-RAY DIFFRACTIONr_scbond_it0.72633218
X-RAY DIFFRACTIONr_scangle_it1.3384.52976
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 2007 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Atight positional0.030.05
Btight positional0.030.05
Ctight positional0.030.05
Atight thermal0.020.5
Btight thermal0.020.5
Ctight thermal0.020.5
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 197 -
Rwork0.316 3623 -
obs--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)
11.899-0.5561-0.04641.9591-0.03690.79630.081-0.0191-0.1239-0.01540.02720.02310.0976-0.1106-0.10820.3092-0.06460.01170.34940.03140.3392-26.66949.4148-6.7111
22.23770.6237-0.42021.669-0.75481.3733-0.0545-0.03480.1425-0.0760.07420.0754-0.132-0.1159-0.01980.39180.01120.0460.29790.02870.3398-17.90182.7377-21.2071
32.02220.7799-0.97912.5181-0.99991.81510.1241-0.1327-0.1622-0.0301-0.1393-0.3708-0.0160.3050.01530.3432-0.00320.05620.4006-0.00610.42328.734856.9954-15.5188
44.3599-0.81561.73523.0284-0.01412.2316-0.0529-0.4871-0.16120.08390.2093-0.1309-0.062-0.2359-0.15630.0703-0.0033-0.0370.23290.06640.1677-5.514336.484418.2965
55.7943-2.0488-2.65041.2776-0.00853.4448-0.40190.1164-0.30180.4966-0.06650.16140.0071-0.23040.46840.5513-0.18040.34890.0846-0.16180.3104-37.792686.47845.6774
63.51142.96471.71135.55353.31865.0015-0.48570.04610.2071-0.39350.24570.3849-0.2867-0.15010.240.1534-0.08130.01330.1237-0.02190.060418.660587.2442-3.8455
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A14 - 279
2X-RAY DIFFRACTION2B14 - 279
3X-RAY DIFFRACTION3C14 - 279
4X-RAY DIFFRACTION4D462 - 581
5X-RAY DIFFRACTION5E463 - 581
6X-RAY DIFFRACTION6F462 - 581

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