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- PDB-1mdl: MANDELATE RACEMASE MUTANT K166R CO-CRYSTALLIZED WITH (R)-MANDELATE -

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Basic information

Entry
Database: PDB / ID: 1mdl
TitleMANDELATE RACEMASE MUTANT K166R CO-CRYSTALLIZED WITH (R)-MANDELATE
ComponentsMANDELATE RACEMASE
KeywordsISOMERASE / MANDELATE PATHWAY / MAGNESIUM
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
(R)-MANDELIC ACID / (S)-MANDELIC ACID / Mandelate racemase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.85 Å
AuthorsClifton, J.G. / Petsko, G.A.
Citation
Journal: Biochemistry / Year: 1995
Title: Mechanism of the reaction catalyzed by mandelate racemase: structure and mechanistic properties of the K166R mutant.
Authors: 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 29, 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: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Mar 14, 2018Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.5Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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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)38,9594
Polymers38,6311
Non-polymers3293
Water3,099172
1
A: MANDELATE RACEMASE
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)311,67432
Polymers309,0458
Non-polymers2,62924
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x,-y,-z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation8_555-y,-x,-z1
crystal symmetry operation5_555-x,y,-z1
crystal symmetry operation2_555-x,-y,z1
Unit cell
Length a, b, c (Å)125.320, 125.320, 106.420
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: 38630.609 Da / Num. of mol.: 1 / Mutation: K166R
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-RMN / (R)-MANDELIC ACID


Mass: 152.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H8O3
#4: Chemical ChemComp-SMN / (S)-MANDELIC ACID


Mass: 152.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHIS IS THE STRUCTURE OF THE MANDELATE RACEMASE MUTANT LYSINE 166 -> ARGININE CO-CRYSTALLIZED WITH ...THIS IS THE STRUCTURE OF THE MANDELATE RACEMASE MUTANT LYSINE 166 -> ARGININE CO-CRYSTALLIZED WITH THE SUBSTRATE (R)-MANDELIC ACID. THE SUBSTRATE THAT IS BOUND AT THE ACTIVE SITE IS RESIDUE 399 FOR CONSISTENCY WITH THE NOMENCLATURE OF PREVIOUS MANDELATE RACEMASE STRUCTURES. IT HAS THE RESIDUE NAME SMN BECAUSE IT IS THE (S)-ISOMER. THE (S)-ENANTIOMER PRESUMABLY AROSE FROM THE SLOW RACEMIZATION OF (R)-MANDELATE. THERE IS A SECOND SUBSTRATE MOLECULE IN THE STRUCTURE; IT IS LOCATED IN THE REGION LEADING TO THE ACTIVE SITE. THIS MOLECULE IS THE (R)-STEREOISOMER. IT IS RESIDUE 398 AND, BY ANALOGY, HAS THE RESIDUE NAME RMN.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 55 %
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
45 mMatrolactate1drop
530 %1reservoirNH4(SO4)2
63 %(v/v)acetone1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Nov 12, 1992
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 33438 / % possible obs: 90.5 % / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Rmerge(I) obs: 0.11
Reflection
*PLUS
Highest resolution: 1.85 Å

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Processing

Software
NameClassification
TNTrefinement
XDSdata reduction
XSCALEdata scaling
RefinementResolution: 1.85→20 Å / σ(F): 1 /
RfactorNum. reflection
Rwork0.184 -
obs-32004
Refinement stepCycle: LAST / Resolution: 1.85→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2700 0 23 172 2895
Refine LS restraints
Refine-IDTypeDev idealWeightNumber
X-RAY DIFFRACTIONt_bond_d0.0190.02
X-RAY DIFFRACTIONt_angle_deg3.133758
X-RAY DIFFRACTIONt_dihedral_angle_d241644
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.020.0260
X-RAY DIFFRACTIONt_gen_planes0.0210.02406
X-RAY DIFFRACTIONt_it0.0832409
X-RAY DIFFRACTIONt_nbd0.0830.110
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.184
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg24
X-RAY DIFFRACTIONt_planar_d0.020.02
X-RAY DIFFRACTIONt_plane_restr0.0210.02

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