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

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Basic information

Entry
Database: PDB / ID: 1mra
TitleMANDELATE RACEMASE MUTANT D270N CO-CRYSTALLIZED WITH (S)-ATROLACTATE
ComponentsMANDELATE RACEMASE
KeywordsRACEMASE / ISOMERASE / MANDELATE PATHWAY / ATROLACTATE / MAGNESIUM RACEMASE
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 putida (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsClifton, J.G. / Petsko, G.A.
Citation
Journal: Biochemistry / Year: 1996
Title: Mechanism of the reaction catalyzed by mandelate racemase: structure and mechanistic properties of the D270N mutant.
Authors: Schafer, S.L. / Barrett, W.C. / Kallarakal, A.T. / Mitra, B. / 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 12, 1996Processing site: BNL
Revision 1.0Aug 1, 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.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.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 14, 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
Water2,000111
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 area30280 Å2
ΔGint-214 kcal/mol
Surface area84270 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)125.000, 125.000, 107.100
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: D270N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (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 / Water


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHIS IS THE STRUCTURE OF THE MANDELATE RACEMASE MUTANT ASPARTATE 270 -> ASPARAGINE CO-CRYSTALLIZED ...THIS IS THE STRUCTURE OF THE MANDELATE RACEMASE MUTANT ASPARTATE 270 -> ASPARAGINE CO-CRYSTALLIZED WITH THE COMPETITIVE INHIBITOR (S)-ATROLACTIC ACID.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 55 %
Crystal growDetails: 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.
Crystal
*PLUS
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop / Details: Mitra, B., (1995) Biochemistry, 34, 2777.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
150 mMTris1drop
210 mM1dropMgCl2
350 mM(S)-atrolactate1drop
413 mg/mlD270N1drop
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: Jul 25, 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 24713 / % possible obs: 74.6 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.171 / Net I/σ(I): 1

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Processing

Software
NameClassification
TNTrefinement
XDSdata reduction
XSCALEdata scaling
RefinementResolution: 2.1→20 Å / Isotropic thermal model: TNT / σ(F): 1 / Stereochemistry target values: TNT
Details: RESIDUES LEU 18 - THR 31: THE ELECTRON DENSITY FOR THE RESIDUES IN THE "FLAP" REGION CONTAINED MULTIPLE BREAKS. IT IS LIKELY THAT THE "FLAP" RESIDUES WERE ACTUALLY PRESENT IN MULTIPLE ...Details: RESIDUES LEU 18 - THR 31: THE ELECTRON DENSITY FOR THE RESIDUES IN THE "FLAP" REGION CONTAINED MULTIPLE BREAKS. IT IS LIKELY THAT THE "FLAP" RESIDUES WERE ACTUALLY PRESENT IN MULTIPLE CONFORMATIONS. HOWEVER, THEY WERE REFINED IN THESE CONFORMATIONS WITH THEIR OCCUPANCIES SET TO 1.0. CONSEQUENTLY, THEIR B-FACTORS ARE GREATER THAN THE REST OF THE PROTEIN. FURTHERMORE, THE LACK OF "ENCLOSING" ELECTRON DENSITY CAUSED MORE SIGNIFICANT GEOMETRIC DEVIATIONS DURING REFINEMENT.
Num. reflection% reflection
obs19219 74.6 %
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2698 0 13 111 2822
Refine LS restraints
Refine-IDTypeDev idealWeightNumber
X-RAY DIFFRACTIONt_bond_d0.0130.02
X-RAY DIFFRACTIONt_angle_deg1.7233745
X-RAY DIFFRACTIONt_dihedral_angle_d251641
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.0120.0259
X-RAY DIFFRACTIONt_gen_planes0.0140.02404
X-RAY DIFFRACTIONt_it8.12753
X-RAY DIFFRACTIONt_nbd0.0030.130
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg25

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