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- PDB-1dtn: MANDELATE RACEMASE MUTANT D270N CO-CRYSTALLIZED WITH (S)-ATROLACTATE -

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Basic information

Entry
Database: PDB / ID: 1dtn
TitleMANDELATE RACEMASE MUTANT D270N CO-CRYSTALLIZED WITH (S)-ATROLACTATE
ComponentsMANDELATE RACEMASE
KeywordsRACEMASE / ISOMERASE / MANDELATE PATHWAY
Function / homology
Function and homology information


mandelate racemase / mandelate racemase activity / mandelate catabolic process / amino acid catabolic process / hydro-lyase activity / carbohydrate catabolic process / magnesium ion binding
Similarity search - Function
Mandelate racemase / Mandelate racemase / muconate lactonizing enzyme family signature 2. / : / Mandelate racemase / muconate lactonizing enzyme family signature 1. / Mandelate racemase/muconate lactonizing enzyme, conserved site / 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 ...Mandelate racemase / Mandelate racemase / muconate lactonizing enzyme family signature 2. / : / Mandelate racemase / muconate lactonizing enzyme family signature 1. / Mandelate racemase/muconate lactonizing enzyme, conserved site / 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
ATROLACTIC ACID (2-PHENYL-LACTIC ACID) / Mandelate racemase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsClifton, J.G. / Petsko, G.A.
Citation
Journal: Biochemistry / Year: 1995
Title: Mechanism of the reaction catalyzed by mandelate racemase: importance of electrophilic catalysis by glutamic acid 317.
Authors: Mitra, B. / Kallarakal, A.T. / Kozarich, J.W. / Gerlt, J.A. / Clifton, J.G. / Petsko, G.A. / Kenyon, G.L.
#1: Journal: Biochemistry / Year: 1991
Title: Mechanism of the Reaction Catalyzed by Mandelate Racemase. 2. Crystal Structure of Mandelate Racemase at 2.5-A Resolution: Identification of the Active Site and Possible Catalytic Residues
Authors: Neidhart, D.J. / Howell, P.L. / Petsko, G.A. / Powers, V.M. / Li, R.S. / Kenyon, G.L. / Gerlt, J.A.
#2: Journal: Nature / Year: 1990
Title: Mandelate Racemase and Muconate Lactonizing Enzyme are Mechanistically Distinct and Structurally Homologous
Authors: Neidhart, D.J. / Kenyon, G.L. / Gerlt, J.A. / Petsko, G.A.
History
DepositionMar 28, 1996Processing site: BNL
Revision 1.0Oct 14, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MANDELATE RACEMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7923
Polymers38,6021
Non-polymers1902
Water1,982110
1
A: MANDELATE RACEMASE
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)310,33724
Polymers308,8138
Non-polymers1,52416
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation5_555-x,y,-z1
crystal symmetry operation6_555x,-y,-z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_555-y,-x,-z1
Buried area28520 Å2
ΔGint-185 kcal/mol
Surface area86280 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)125.500, 125.500, 107.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

#1: Protein MANDELATE RACEMASE


Mass: 38601.613 Da / Num. of mol.: 1 / Mutation: E317Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Description: TRC PROMOTER / Gene: MANDELATE RACEMASE / Plasmid: PKT230 / Gene (production host): MANDELATE RACEMASE / Production host: Escherichia coli (E. coli) / References: UniProt: P11444, mandelate racemase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-APG / ATROLACTIC ACID (2-PHENYL-LACTIC ACID)


Mass: 166.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHIS IS THE STRUCTURE OF THE MANDELATE RACEMASE MUTANT GLUTAMATE 317 -> GLUTAMINE CO-CRYSTALLIZED ...THIS IS THE STRUCTURE OF THE MANDELATE RACEMASE MUTANT GLUTAMATE 317 -> GLUTAMINE CO-CRYSTALLIZED WITH THE COMPETITIVE INHIBITOR (S)- ATROLACTIC ACID. THE INHIBITOR (ALSO CALLED (S)-ALPHA-METHYLMANDELIC ACID) IS RESIDUE 399. THE INHIBITOR CONSTANT (K SUB I) FOR (S)-ATROLACTATE IS APPROXIMATELY 0.2 MILLIMOLAR; CRYSTALS WERE OBTAINED FROM A SOLUTION THAT CONTAINED 5 MILLIMOLAR INHIBITOR.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.73 Å3/Da / Density % sol: 55 %
Crystal
*PLUS
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
150 mMTris1drop
210 mM1dropMgCl2
350 mM(S)-atrolactate1drop
413 mg/mlE317Q1drop
55 mMatrolactate1drop
630 %1reservoirNH4(SO4)2
73 %(v/v)acetone1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Jun 3, 1992
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 24924 / % possible obs: 85.3 % / Observed criterion σ(I): 1 / Redundancy: 2.7 % / Rmerge(I) obs: 0.13

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Processing

Software
NameClassification
X-PLORmodel building
TNTrefinement
X-PLORrefinement
XDSdata reduction
XSCALEdata scaling
X-PLORphasing
RefinementResolution: 2.1→20 Å / σ(F): 1
Details: RANGE_OF_ATOMS_OR_RESIDUES: LEU 18 - ALA 32 THE ELECTRON DENSITY FOR THE RESIDUES IN THE "FLAP" REGION (LEU 18 - ALA 32) INDICATED THAT THESE RESIDUES WERE PRESENT IN TWO DIFFERENT ...Details: RANGE_OF_ATOMS_OR_RESIDUES: LEU 18 - ALA 32 THE ELECTRON DENSITY FOR THE RESIDUES IN THE "FLAP" REGION (LEU 18 - ALA 32) INDICATED THAT THESE RESIDUES WERE PRESENT IN TWO DIFFERENT CONFORMATIONS. THE OCCUPANCIES OF THE TWO CONFORMATIONS WERE REFINED WITH X-PLOR, WHICH DID NOT KEEP THE SUMS OF THE TWO OCCUPANCIES EQUAL TO 1.0. AFTER THAT REFINEMENT, THE STRUCTURE WAS REFINED USING TNT, KEEPING THE OCCUPANCIES (FROM X-PLOR) CONSTANT. INSTEAD, THE B-FACTORS WERE REFINED.
RfactorNum. reflection% reflection
Rwork0.171 --
all-24924 -
obs-20034 85.3 %
Displacement parametersBiso mean: 19.3 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2698 0 13 110 2821
Refine LS restraints
Refine-IDTypeDev idealWeightNumber
X-RAY DIFFRACTIONt_bond_d0.010.02
X-RAY DIFFRACTIONt_angle_deg2.233902
X-RAY DIFFRACTIONt_dihedral_angle_d241701
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.0090.0259
X-RAY DIFFRACTIONt_gen_planes0.0170.02422
X-RAY DIFFRACTIONt_it1.72403
X-RAY DIFFRACTIONt_nbd0.0480.18
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.171
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_planar_d0.0090.02
X-RAY DIFFRACTIONt_plane_restr0.0170.02

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