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- PDB-3vcc: CRYSTAL STRUCTURE OF D-Galacturonate Dehydratase from GEOBACILLUS... -

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Basic information

Entry
Database: PDB / ID: 3vcc
TitleCRYSTAL STRUCTURE OF D-Galacturonate Dehydratase from GEOBACILLUS SP. complexed with Mg
ComponentsMandelate racemase/muconate lactonizing protein
KeywordsMETAL BINDING PROTEIN / enolase fold
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
DI(HYDROXYETHYL)ETHER / Mandelate racemase/muconate lactonizing protein
Similarity search - Component
Biological speciesPaenibacillus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsFedorov, A.A. / Fedorov, E.V. / Groninger-Poe, F. / Gerlt, J.A. / Almo, S.C.
CitationJournal: To be Published
Title: CRYSTAL STRUCTURE OF D-Galacturonate Dehydratase from GEOBACILLUS SP. complexed with Mg
Authors: Fedorov, A.A. / Fedorov, E.V. / Groninger-Poe, F. / Gerlt, J.A. / Almo, S.C.
History
DepositionJan 3, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 9, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 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_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_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: Mandelate racemase/muconate lactonizing protein
B: Mandelate racemase/muconate lactonizing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,0507
Polymers87,8462
Non-polymers2035
Water9,908550
1
A: Mandelate racemase/muconate lactonizing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9723
Polymers43,9231
Non-polymers492
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mandelate racemase/muconate lactonizing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0784
Polymers43,9231
Non-polymers1553
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2440 Å2
ΔGint-46 kcal/mol
Surface area30270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.347, 65.985, 75.636
Angle α, β, γ (deg.)90.00, 93.56, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Mandelate racemase/muconate lactonizing protein


Mass: 43923.195 Da / Num. of mol.: 2
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
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 550 / 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: 2.19 Å3/Da / Density % sol: 43.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 25% 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: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 29, 2010
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.64→40.525 Å / Num. all: 84573 / Num. obs: 84573 / % possible obs: 90.93 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
CBASSdata collection
BALBESphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3P3B

3p3b


Resolution: 1.64→40.525 Å / SU ML: 0.41 / σ(F): 0 / Phase error: 23.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2164 4220 4.99 %RANDOM
Rwork0.1793 ---
all0.1812 84573 --
obs0.1812 84573 90.93 %-
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 29.333 Å2 / ksol: 0.34 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.4137 Å2-0 Å2-4.7336 Å2
2---1.2534 Å20 Å2
3---1.6671 Å2
Refinement stepCycle: LAST / Resolution: 1.64→40.525 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6072 0 11 550 6633
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076327
X-RAY DIFFRACTIONf_angle_d1.078592
X-RAY DIFFRACTIONf_dihedral_angle_d13.0192287
X-RAY DIFFRACTIONf_chiral_restr0.075901
X-RAY DIFFRACTIONf_plane_restr0.0041131
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6397-1.65830.3775360.3879754X-RAY DIFFRACTION26
1.6583-1.67780.3534540.36261236X-RAY DIFFRACTION42
1.6778-1.69830.373810.32591512X-RAY DIFFRACTION52
1.6983-1.71980.4158910.31781902X-RAY DIFFRACTION64
1.7198-1.74240.34081180.30512157X-RAY DIFFRACTION74
1.7424-1.76630.29041400.29062462X-RAY DIFFRACTION85
1.7663-1.79150.31091400.28732716X-RAY DIFFRACTION92
1.7915-1.81820.28131400.27662835X-RAY DIFFRACTION97
1.8182-1.84670.3091480.25482874X-RAY DIFFRACTION98
1.8467-1.87690.32751550.23072927X-RAY DIFFRACTION99
1.8769-1.90930.26151400.22132902X-RAY DIFFRACTION99
1.9093-1.9440.2721470.20852938X-RAY DIFFRACTION99
1.944-1.98140.25381340.19962946X-RAY DIFFRACTION100
1.9814-2.02190.23461700.19062895X-RAY DIFFRACTION100
2.0219-2.06580.25431500.18732949X-RAY DIFFRACTION100
2.0658-2.11390.23551600.17242944X-RAY DIFFRACTION100
2.1139-2.16670.22221830.17052901X-RAY DIFFRACTION100
2.1667-2.22530.19481510.16012950X-RAY DIFFRACTION100
2.2253-2.29080.23331470.16512956X-RAY DIFFRACTION100
2.2908-2.36470.19071490.16242954X-RAY DIFFRACTION100
2.3647-2.44920.2141490.17992944X-RAY DIFFRACTION100
2.4492-2.54730.23091550.17562933X-RAY DIFFRACTION100
2.5473-2.66320.24731650.17822923X-RAY DIFFRACTION100
2.6632-2.80360.20631750.18442958X-RAY DIFFRACTION100
2.8036-2.97920.24311590.18852948X-RAY DIFFRACTION100
2.9792-3.20910.2071630.18682939X-RAY DIFFRACTION100
3.2091-3.53190.21011690.17522961X-RAY DIFFRACTION100
3.5319-4.04250.18231520.1492971X-RAY DIFFRACTION100
4.0425-5.09160.16711360.13793010X-RAY DIFFRACTION100
5.0916-40.5370.16771630.15923056X-RAY DIFFRACTION100

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