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- PDB-5fpz: The structure of KdgF from Yersinia enterocolitica with malonate ... -

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Basic information

Entry
Database: PDB / ID: 5fpz
TitleThe structure of KdgF from Yersinia enterocolitica with malonate bound in the active site.
ComponentsPECTIN DEGRADATION PROTEIN
KeywordsHYDROLASE / KDGF / PECTIN / ALGINATE / URONATE SUGAR METABOLISM / CUPIN
Function / homology
Function and homology information


Pectin degradation protein KdgF / : / Cupin 2, conserved barrel / Cupin domain / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
MALONIC ACID / NICKEL (II) ION / Pectin degradation protein
Similarity search - Component
Biological speciesYERSINIA ENTEROCOLITICA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsHobbs, J.K. / Lee, S.M. / Robb, M. / Hof, F. / Barr, C. / Abe, K.T. / Hehemann, J.H. / McLean, R. / Abbott, D.W. / Boraston, A.B.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Kdgf, the Missing Link in the Microbial Metabolism of Uronate Sugars from Pectin and Alginate.
Authors: Hobbs, J.K. / Lee, S.M. / Robb, M. / Hof, F. / Barr, C. / Abe, K.T. / Hehemann, J. / Mclean, R. / Abbott, D.W. / Boraston, A.B.
History
DepositionDec 3, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2016Group: Database references
Revision 1.2Jun 15, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.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_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_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: PECTIN DEGRADATION PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6493
Polymers12,4861
Non-polymers1632
Water3,531196
1
A: PECTIN DEGRADATION PROTEIN
hetero molecules

A: PECTIN DEGRADATION PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2986
Polymers24,9722
Non-polymers3264
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
Buried area4190 Å2
ΔGint-60.9 kcal/mol
Surface area9820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.190, 60.190, 67.831
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-2033-

HOH

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Components

#1: Protein PECTIN DEGRADATION PROTEIN / KDGF


Mass: 12486.178 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) YERSINIA ENTEROCOLITICA (bacteria) / Strain: SUBSP. ENTEROCOLITICA 8081 / References: UniProt: A1JMF7
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID


Mass: 104.061 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 2.84 Å3/Da / Density % sol: 56.7 % / Description: NONE

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.5→53 Å / Num. obs: 23188 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.3
Reflection shellResolution: 1.5→1.54 Å / Redundancy: 4 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.7 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5FPX

5fpx


Resolution: 1.5→52.13 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.027 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.064 / ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.20488 1185 5.1 %RANDOM
Rwork0.16975 ---
obs0.17139 21989 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.722 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å2-0.03 Å20 Å2
2---0.07 Å20 Å2
3---0.22 Å2
Refinement stepCycle: LAST / Resolution: 1.5→52.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms876 0 8 196 1080
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.019904
X-RAY DIFFRACTIONr_bond_other_d0.0020.02864
X-RAY DIFFRACTIONr_angle_refined_deg1.4171.9381217
X-RAY DIFFRACTIONr_angle_other_deg0.753.0021976
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2715111
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.72324.88945
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.04415162
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.16154
X-RAY DIFFRACTIONr_chiral_restr0.0920.2129
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021030
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02208
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_it1.1021.519441
X-RAY DIFFRACTIONr_mcbond_other1.0851.515440
X-RAY DIFFRACTIONr_mcangle_it1.7882.271550
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.9261.768463
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.613 92 -
Rwork0.553 1602 -
obs--100 %

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