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- PDB-3qpe: Crystal structure of Galacturonate Dehydratase from GEOBACILLUS S... -

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Basic information

Entry
Database: PDB / ID: 3qpe
TitleCrystal structure of Galacturonate Dehydratase from GEOBACILLUS SP. complexed with D-Galacturonate and 5-keto-4-deoxy-D-Galacturonate
ComponentsMandelate racemase/muconate lactonizing protein
KeywordsMETAL BINDING PROTEIN / Enolase fold / Galacturonate Dehydratase
Function / homology
Function and homology information


hydro-lyase activity / metal ion binding
Similarity search - Function
: / Mandelate racemase/muconate lactonizing enzyme, C-terminal / Mandelate racemase / muconate lactonizing enzyme, C-terminal domain / Enolase C-terminal domain-like / Enolase C-terminal domain-like / Enolase-like C-terminal domain / Enolase-like, N-terminal domain / Enolase-like, N-terminal / Enolase-like, C-terminal domain superfamily / Enolase-like; domain 1 ...: / Mandelate racemase/muconate lactonizing enzyme, C-terminal / Mandelate racemase / muconate lactonizing enzyme, C-terminal domain / Enolase C-terminal domain-like / Enolase C-terminal domain-like / Enolase-like C-terminal domain / Enolase-like, N-terminal domain / Enolase-like, N-terminal / Enolase-like, C-terminal domain superfamily / Enolase-like; domain 1 / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
4-deoxy-L-threo-hex-5-ulosuronic acid / D-galacturonic acid / Mandelate racemase/muconate lactonizing protein
Similarity search - Component
Biological speciesPaenibacillus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.796 Å
AuthorsFedorov, A.A. / Fedorov, E.V. / Mills-Groninger, F. / Gerlt, J.A. / Almo, S.C.
CitationJournal: To be Published
Title: Crystal structure of Galacturonate Dehydratase from GEOBACILLUS SP. complexed with D-Galacturonate and 5-keto-4-deoxy-D-Galacturonate
Authors: Fedorov, A.A. / Fedorov, E.V. / Mills-Groninger, F. / Gerlt, J.A. / Almo, S.C.
History
DepositionFeb 12, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2012Provider: repository / Type: Initial release
Revision 2.0Jul 1, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.type / _entity.src_method / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _struct_conn.ptnr2_label_atom_id / _struct_ref_seq_dif.details
Revision 2.1Sep 13, 2023Group: 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_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_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_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: Mandelate racemase/muconate lactonizing protein
B: Mandelate racemase/muconate lactonizing protein
C: Mandelate racemase/muconate lactonizing protein
D: Mandelate racemase/muconate lactonizing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,70217
Polymers175,6934
Non-polymers1,00913
Water13,601755
1
A: Mandelate racemase/muconate lactonizing protein
B: Mandelate racemase/muconate lactonizing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,3148
Polymers87,8462
Non-polymers4676
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-36 kcal/mol
Surface area29190 Å2
2
C: Mandelate racemase/muconate lactonizing protein
D: Mandelate racemase/muconate lactonizing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,3889
Polymers87,8462
Non-polymers5427
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3520 Å2
ΔGint-45 kcal/mol
Surface area29430 Å2
Unit cell
Length a, b, c (Å)158.019, 66.265, 154.609
Angle α, β, γ (deg.)90.00, 95.73, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein / Sugars , 2 types, 5 molecules ABCD

#1: Protein
Mandelate racemase/muconate lactonizing protein


Mass: 43923.195 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paenibacillus sp. (bacteria) / Strain: Y412MC10 / Gene: GYMC10_3367 / Production host: Escherichia coli (E. coli) / References: UniProt: D3EID5
#3: Sugar ChemComp-DGU / D-galacturonic acid / D-Galacturonate / D-Galacturonic acid


Type: D-saccharide / Mass: 194.139 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H10O7

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Non-polymers , 4 types, 767 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-D54 / 4-deoxy-L-threo-hex-5-ulosuronic acid / 5-keto-4-deoxy-D-Galacturonate


Mass: 176.124 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H8O6
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 755 / 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: 2.29 Å3/Da / Density % sol: 46.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 3350, 0.1M Tris, 0.2M Magnesium Chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 2, 2010
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.796→39.03 Å / Num. all: 147514 / Num. obs: 147514 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
BALBESphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3P3B

3p3b


Resolution: 1.796→39.03 Å / SU ML: 0.29 / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2696 7385 5.01 %RANDOM
Rwork0.221 ---
all0.2235 147514 --
obs0.2235 147514 99.4 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.076 Å2 / ksol: 0.344 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-11.5966 Å2-0 Å2-7.1422 Å2
2---9.6582 Å2-0 Å2
3----1.9384 Å2
Refinement stepCycle: LAST / Resolution: 1.796→39.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11973 0 63 755 12791
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00712343
X-RAY DIFFRACTIONf_angle_d1.03716729
X-RAY DIFFRACTIONf_dihedral_angle_d13.6464504
X-RAY DIFFRACTIONf_chiral_restr0.0691769
X-RAY DIFFRACTIONf_plane_restr0.0042191
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.796-1.81690.41832080.40544072X-RAY DIFFRACTION87
1.8169-1.83820.46452330.39584693X-RAY DIFFRACTION99
1.8382-1.86060.41782530.38314574X-RAY DIFFRACTION99
1.8606-1.88420.40682180.36754702X-RAY DIFFRACTION100
1.8842-1.9090.40542310.35344690X-RAY DIFFRACTION100
1.909-1.93510.37142400.3464636X-RAY DIFFRACTION100
1.9351-1.96280.37322720.31744622X-RAY DIFFRACTION100
1.9628-1.99210.35332500.31054716X-RAY DIFFRACTION100
1.9921-2.02320.35192320.29594667X-RAY DIFFRACTION100
2.0232-2.05640.36552590.28424659X-RAY DIFFRACTION100
2.0564-2.09180.32312510.27284641X-RAY DIFFRACTION100
2.0918-2.12990.29842460.26174743X-RAY DIFFRACTION100
2.1299-2.17080.31722520.25784600X-RAY DIFFRACTION100
2.1708-2.21510.29272200.24034730X-RAY DIFFRACTION100
2.2151-2.26330.32142590.24214698X-RAY DIFFRACTION100
2.2633-2.31590.31062380.23274673X-RAY DIFFRACTION100
2.3159-2.37380.30612410.22334686X-RAY DIFFRACTION100
2.3738-2.4380.28362780.22734651X-RAY DIFFRACTION100
2.438-2.50970.29042630.2234662X-RAY DIFFRACTION100
2.5097-2.59070.30012340.22794715X-RAY DIFFRACTION100
2.5907-2.68330.29492250.22344694X-RAY DIFFRACTION100
2.6833-2.79070.25972370.22914675X-RAY DIFFRACTION100
2.7907-2.91770.32552600.2384707X-RAY DIFFRACTION100
2.9177-3.07150.27582660.21944702X-RAY DIFFRACTION100
3.0715-3.26380.29782460.224717X-RAY DIFFRACTION100
3.2638-3.51570.24532670.1984706X-RAY DIFFRACTION100
3.5157-3.86920.20682570.17884727X-RAY DIFFRACTION100
3.8692-4.42840.20122410.16284751X-RAY DIFFRACTION100
4.4284-5.57670.18682610.15354767X-RAY DIFFRACTION100
5.5767-39.03910.19252470.17394853X-RAY DIFFRACTION99

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