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- PDB-3mqt: Crystal structure of a mandelate racemase/muconate lactonizing en... -

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Basic information

Entry
Database: PDB / ID: 3mqt
TitleCrystal structure of a mandelate racemase/muconate lactonizing enzyme from Shewanella pealeana
ComponentsMandelate racemase/muconate lactonizing protein
KeywordsISOMERASE / PSI-II / NYSGXRC / mandelate racemase / muconate lactonizing enzyme / Structural Genomics / Protein Structure Initiative / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


hydro-lyase activity / carbohydrate catabolic process / magnesium ion binding
Similarity search - Function
: / Mandelate racemase/muconate lactonizing enzyme, N-terminal domain / Mandelate racemase / muconate lactonizing enzyme, N-terminal domain / 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 ...: / Mandelate racemase/muconate lactonizing enzyme, N-terminal domain / Mandelate racemase / muconate lactonizing enzyme, N-terminal domain / 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
Mandelate racemase/muconate lactonizing protein
Similarity search - Component
Biological speciesShewanella pealeana (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsAgarwal, R. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal STRUCTURE OF A MANDELATE RACEMASE/MUCONATE LACTONIZING ENZYME FROM SHEWANELLA PEALEANA
Authors: Agarwal, R. / Burley, S.K. / Swaminathan, S.
History
DepositionApr 28, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _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
Revision 1.3Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
E: Mandelate racemase/muconate lactonizing protein
F: Mandelate racemase/muconate lactonizing protein
G: Mandelate racemase/muconate lactonizing protein
H: Mandelate racemase/muconate lactonizing protein
I: Mandelate racemase/muconate lactonizing protein
J: Mandelate racemase/muconate lactonizing protein
K: Mandelate racemase/muconate lactonizing protein
L: Mandelate racemase/muconate lactonizing protein
M: Mandelate racemase/muconate lactonizing protein
N: Mandelate racemase/muconate lactonizing protein
O: Mandelate racemase/muconate lactonizing protein
P: Mandelate racemase/muconate lactonizing protein
Q: Mandelate racemase/muconate lactonizing protein
R: Mandelate racemase/muconate lactonizing protein
S: Mandelate racemase/muconate lactonizing protein
T: Mandelate racemase/muconate lactonizing protein
U: Mandelate racemase/muconate lactonizing protein
V: Mandelate racemase/muconate lactonizing protein
W: Mandelate racemase/muconate lactonizing protein
X: Mandelate racemase/muconate lactonizing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,068,04336
Polymers1,067,75124
Non-polymers29212
Water24,9151383
1
A: Mandelate racemase/muconate lactonizing protein
B: Mandelate racemase/muconate lactonizing protein
C: Mandelate racemase/muconate lactonizing protein
D: Mandelate racemase/muconate lactonizing protein
E: Mandelate racemase/muconate lactonizing protein
F: Mandelate racemase/muconate lactonizing protein
G: Mandelate racemase/muconate lactonizing protein
H: Mandelate racemase/muconate lactonizing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)356,06314
Polymers355,9178
Non-polymers1466
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3140 Å2
ΔGint-23 kcal/mol
Surface area27730 Å2
2
I: Mandelate racemase/muconate lactonizing protein
J: Mandelate racemase/muconate lactonizing protein
K: Mandelate racemase/muconate lactonizing protein
L: Mandelate racemase/muconate lactonizing protein
M: Mandelate racemase/muconate lactonizing protein
N: Mandelate racemase/muconate lactonizing protein
V: Mandelate racemase/muconate lactonizing protein
W: Mandelate racemase/muconate lactonizing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)356,01412
Polymers355,9178
Non-polymers974
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
O: Mandelate racemase/muconate lactonizing protein
P: Mandelate racemase/muconate lactonizing protein
Q: Mandelate racemase/muconate lactonizing protein
R: Mandelate racemase/muconate lactonizing protein
S: Mandelate racemase/muconate lactonizing protein
T: Mandelate racemase/muconate lactonizing protein
U: Mandelate racemase/muconate lactonizing protein
X: Mandelate racemase/muconate lactonizing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)355,96610
Polymers355,9178
Non-polymers492
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)111.164, 146.142, 158.710
Angle α, β, γ (deg.)98.47, 96.80, 105.04
Int Tables number1
Space group name H-MP1
DetailsOctamer

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Components

#1: Protein ...
Mandelate racemase/muconate lactonizing protein


Mass: 44489.641 Da / Num. of mol.: 24
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella pealeana (bacteria) / Strain: ATCC700345 / Gene: Spea_3246 / Plasmid: pSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 RIPL / References: UniProt: A8H7M5
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1383 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 45.94 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M MgCl2, 0.1M Tris, pH 8.5, 30% PEG 4K, Dioxane, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 1, 2010 / Details: mirrors
RadiationMonochromator: Si-III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 484982 / Num. obs: 484982 / % possible obs: 89 % / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 6.7
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2 / Num. unique all: 25144 / % possible all: 46

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Processing

Software
NameVersionClassification
CBASSdata collection
CCP4model building
MOLREPphasing
Cootmodel building
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MKC

3mkc


Resolution: 2.1→49.33 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.92 / SU B: 4.364 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21318 4843 1 %RANDOM
Rwork0.18526 ---
obs0.18554 478270 100 %-
all-484982 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.086 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å2-0.86 Å2-0.15 Å2
2--0.28 Å20.42 Å2
3----0.37 Å2
Refinement stepCycle: LAST / Resolution: 2.1→49.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms71547 0 12 1383 72942
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02273203
X-RAY DIFFRACTIONr_angle_refined_deg1.3041.94899273
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.41559015
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.65524.7893408
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.6911512648
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.32315360
X-RAY DIFFRACTIONr_chiral_restr0.10.211007
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.02155260
X-RAY DIFFRACTIONr_mcbond_it1.2851.544931
X-RAY DIFFRACTIONr_mcangle_it2.252272321
X-RAY DIFFRACTIONr_scbond_it4.055328272
X-RAY DIFFRACTIONr_scangle_it6.0084.526952
LS refinement shellResolution: 2.104→2.159 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 181 -
Rwork0.252 16950 -
obs-484982 100 %

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