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- PDB-4wkm: AmpR effector binding domain from Citrobacter freundii bound to U... -

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Basic information

Entry
Database: PDB / ID: 4wkm
TitleAmpR effector binding domain from Citrobacter freundii bound to UDP-MurNAc-pentapeptide
Components
  • ALA-FGA-API-DAL-DAL
  • LysR family transcriptional regulator
KeywordsTRANSCRIPTION / LysR-type transcriptional regulator / LTTR / UDP-MurNAc-pentapeptide
Function / homologyPeriplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta / N-acetyl-alpha-muramic acid / polypeptide(D) / :
Function and homology information
Biological speciesCitrobacter freundii ATCC 8090 = MTCC 1658 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsVadlamani, G. / Reeve, T.M. / Mark, B.L.
Funding support Canada, 2items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
Cystic Fibrosis Canada Canada
CitationJournal: J.Biol.Chem. / Year: 2015
Title: The beta-Lactamase Gene Regulator AmpR Is a Tetramer That Recognizes and Binds the d-Ala-d-Ala Motif of Its Repressor UDP-N-acetylmuramic Acid (MurNAc)-pentapeptide.
Authors: Vadlamani, G. / Thomas, M.D. / Patel, T.R. / Donald, L.J. / Reeve, T.M. / Stetefeld, J. / Standing, K.G. / Vocadlo, D.J. / Mark, B.L.
History
DepositionOct 2, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 17, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 11, 2015Group: Structure summary
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations / Source and taxonomy
Category: chem_comp / entity_src_gen ...chem_comp / entity_src_gen / pdbx_audit_support / pdbx_database_related / pdbx_entity_src_syn / pdbx_struct_oper_list
Item: _chem_comp.type / _entity_src_gen.pdbx_alt_source_flag ..._chem_comp.type / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_related.content_type / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 3.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LysR family transcriptional regulator
B: LysR family transcriptional regulator
C: LysR family transcriptional regulator
D: LysR family transcriptional regulator
E: LysR family transcriptional regulator
F: LysR family transcriptional regulator
G: LysR family transcriptional regulator
H: LysR family transcriptional regulator
I: ALA-FGA-API-DAL-DAL
J: ALA-FGA-API-DAL-DAL
K: ALA-FGA-API-DAL-DAL
L: ALA-FGA-API-DAL-DAL
M: ALA-FGA-API-DAL-DAL
N: ALA-FGA-API-DAL-DAL
O: ALA-FGA-API-DAL-DAL
P: ALA-FGA-API-DAL-DAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)204,70931
Polymers201,71816
Non-polymers2,99115
Water18,7901043
1
A: LysR family transcriptional regulator
B: LysR family transcriptional regulator
I: ALA-FGA-API-DAL-DAL
J: ALA-FGA-API-DAL-DAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1087
Polymers50,4304
Non-polymers6793
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: LysR family transcriptional regulator
D: LysR family transcriptional regulator
K: ALA-FGA-API-DAL-DAL
L: ALA-FGA-API-DAL-DAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2008
Polymers50,4304
Non-polymers7714
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: LysR family transcriptional regulator
F: LysR family transcriptional regulator
M: ALA-FGA-API-DAL-DAL
N: ALA-FGA-API-DAL-DAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2008
Polymers50,4304
Non-polymers7714
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: LysR family transcriptional regulator
H: LysR family transcriptional regulator
O: ALA-FGA-API-DAL-DAL
P: ALA-FGA-API-DAL-DAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2008
Polymers50,4304
Non-polymers7714
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.700, 183.600, 197.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
LysR family transcriptional regulator


Mass: 24682.244 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Citrobacter freundii ATCC 8090 = MTCC 1658 (bacteria)
Gene: D186_13659 / Production host: Escherichia coli (E. coli) / References: UniProt: K8QNC4
#2: Polypeptide(D)
ALA-FGA-API-DAL-DAL


Mass: 532.544 Da / Num. of mol.: 8 / Source method: obtained synthetically
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#4: Sugar
ChemComp-MUB / N-acetyl-alpha-muramic acid / N-acetyl-muramic acid / N-ACETYLMURAMIC ACID


Type: D-saccharide, alpha linking / Mass: 293.270 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C11H19NO8
IdentifierTypeProgram
a-D-GlcpNAc3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
MurNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1043 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.88 Å3/Da / Density % sol: 57.34 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: AmpR-EBD concentration: 4.5 mg/ml, mixed with 5mM UDP-MurNAc-pentapeptide, then crystallized in 10% PEG 3350, 9% glycerol and 100 mM MES pH 6.2.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jun 25, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.15→59.33 Å / Num. obs: 121101 / % possible obs: 97.7 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 8.3
Reflection shellResolution: 2.15→2.27 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.497 / Mean I/σ(I) obs: 3 / % possible all: 98

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.9pre_1669) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3kos

3kos


Resolution: 2.15→52.956 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2542 2722 2.25 %Random
Rwork0.2009 ---
obs0.2022 120936 96.7 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.15→52.956 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12527 0 138 1043 13708
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01312998
X-RAY DIFFRACTIONf_angle_d1.45617734
X-RAY DIFFRACTIONf_dihedral_angle_d14.7024559
X-RAY DIFFRACTIONf_chiral_restr0.0572013
X-RAY DIFFRACTIONf_plane_restr0.0082255
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.18910.36631330.30986033X-RAY DIFFRACTION95
2.1891-2.23120.35231590.29426249X-RAY DIFFRACTION98
2.2312-2.27680.34781380.2766190X-RAY DIFFRACTION98
2.2768-2.32630.32171390.26096335X-RAY DIFFRACTION98
2.3263-2.38040.30091590.26196193X-RAY DIFFRACTION99
2.3804-2.43990.33041360.24426322X-RAY DIFFRACTION98
2.4399-2.50590.27961440.2376281X-RAY DIFFRACTION98
2.5059-2.57960.24591420.22216216X-RAY DIFFRACTION98
2.5796-2.66290.31471480.21066259X-RAY DIFFRACTION98
2.6629-2.7580.27951530.20446264X-RAY DIFFRACTION98
2.758-2.86850.26811340.21086237X-RAY DIFFRACTION97
2.8685-2.9990.28031440.20946274X-RAY DIFFRACTION97
2.999-3.15710.23561430.20946215X-RAY DIFFRACTION97
3.1571-3.35490.25081450.20226211X-RAY DIFFRACTION97
3.3549-3.61380.26871420.18736198X-RAY DIFFRACTION96
3.6138-3.97740.24461350.17596233X-RAY DIFFRACTION96
3.9774-4.55270.18691500.1516162X-RAY DIFFRACTION95
4.5527-5.73480.19031360.1546195X-RAY DIFFRACTION94
5.7348-52.97160.22331420.19096147X-RAY DIFFRACTION90

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