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- PDB-3v5c: Crystal structure of the mutant E234A of Galacturonate Dehydratas... -

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Basic information

Entry
Database: PDB / ID: 3v5c
TitleCrystal structure of the mutant E234A of Galacturonate Dehydratase from GEOBACILLUS SP. complexed with Mg
ComponentsMandelate racemase/muconate lactonizing protein
KeywordsLYASE / enolase fold / Galacturonate Dehydratase / double MG site
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: 1.53 Å
AuthorsFedorov, A.A. / Fedorov, E.V. / Groninger-Poe, F. / Gerlt, J.A. / Almo, S.C.
CitationJournal: To be Published
Title: Crystal structure of the mutant E234A of 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
DepositionDec 16, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2012Provider: 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
C: Mandelate racemase/muconate lactonizing protein
D: Mandelate racemase/muconate lactonizing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,26717
Polymers175,4614
Non-polymers80713
Water26,9861498
1
A: Mandelate racemase/muconate lactonizing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9963
Polymers43,8651
Non-polymers1302
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Mandelate racemase/muconate lactonizing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1506
Polymers43,8651
Non-polymers2855
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Mandelate racemase/muconate lactonizing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2085
Polymers43,8651
Non-polymers3434
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Mandelate racemase/muconate lactonizing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9143
Polymers43,8651
Non-polymers492
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)154.271, 65.863, 151.218
Angle α, β, γ (deg.)90.00, 94.17, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-1076-

HOH

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Components

#1: Protein
Mandelate racemase/muconate lactonizing protein


Mass: 43865.160 Da / Num. of mol.: 4 / Mutation: E234A
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.: 7 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1498 / 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: 2.18 Å3/Da / Density % sol: 43.67 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 8.5
Details: 25% PEG3350, 0.1M Tris, 0.2M sodium chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP

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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: Dec 2, 2011
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.53→40.466 Å / Num. all: 199609 / Num. obs: 199609 / % possible obs: 87.59 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
CBASSdata collection
BALBESphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3P3B

3p3b


Resolution: 1.53→40.466 Å / SU ML: 0.19 / σ(F): 0 / Phase error: 22.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2161 10061 5.04 %RANDOM
Rwork0.1851 ---
all0.1866 199609 --
obs0.1866 199609 87.59 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.936 Å2 / ksol: 0.355 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.1305 Å2-0 Å2-0.499 Å2
2---0.0017 Å20 Å2
3---1.1321 Å2
Refinement stepCycle: LAST / Resolution: 1.53→40.466 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11998 0 49 1498 13545
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00612516
X-RAY DIFFRACTIONf_angle_d1.06116971
X-RAY DIFFRACTIONf_dihedral_angle_d11.9284553
X-RAY DIFFRACTIONf_chiral_restr0.0721784
X-RAY DIFFRACTIONf_plane_restr0.0042230
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.53-1.54740.28461010.25271747X-RAY DIFFRACTION25
1.5474-1.56560.2961270.25152546X-RAY DIFFRACTION35
1.5656-1.58470.2881970.24273327X-RAY DIFFRACTION47
1.5847-1.60470.29752020.2474110X-RAY DIFFRACTION57
1.6047-1.62590.2692440.2424782X-RAY DIFFRACTION67
1.6259-1.64810.26773070.23925577X-RAY DIFFRACTION77
1.6481-1.67170.28713260.23146339X-RAY DIFFRACTION89
1.6717-1.69660.25683670.21916712X-RAY DIFFRACTION94
1.6966-1.72310.2953790.21986893X-RAY DIFFRACTION97
1.7231-1.75140.24753660.2177044X-RAY DIFFRACTION97
1.7514-1.78160.24313890.21557032X-RAY DIFFRACTION98
1.7816-1.8140.26343620.20517027X-RAY DIFFRACTION98
1.814-1.84890.26064120.20836974X-RAY DIFFRACTION98
1.8489-1.88660.24483570.20267028X-RAY DIFFRACTION97
1.8866-1.92760.253670.19837070X-RAY DIFFRACTION98
1.9276-1.97250.23243880.1946887X-RAY DIFFRACTION97
1.9725-2.02180.21283760.1897018X-RAY DIFFRACTION97
2.0218-2.07650.20913570.19276920X-RAY DIFFRACTION96
2.0765-2.13760.2293810.18566963X-RAY DIFFRACTION96
2.1376-2.20660.21273530.18546942X-RAY DIFFRACTION96
2.2066-2.28540.21593780.18136904X-RAY DIFFRACTION96
2.2854-2.37690.22543400.17776917X-RAY DIFFRACTION96
2.3769-2.48510.22493510.17726944X-RAY DIFFRACTION96
2.4851-2.61610.20163710.18266991X-RAY DIFFRACTION96
2.6161-2.77990.22083790.18686980X-RAY DIFFRACTION97
2.7799-2.99450.21343630.18797079X-RAY DIFFRACTION97
2.9945-3.29570.21643690.18537037X-RAY DIFFRACTION97
3.2957-3.77230.18823680.16637063X-RAY DIFFRACTION97
3.7723-4.75160.17514140.14957252X-RAY DIFFRACTION100
4.7516-40.480.19833700.18437443X-RAY DIFFRACTION99

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