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- PDB-4m6u: P. putida mandelate racemase co-crystallized with tartronic acid -

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Basic information

Entry
Database: PDB / ID: 4m6u
TitleP. putida mandelate racemase co-crystallized with tartronic acid
ComponentsMandelate racemase
KeywordsISOMERASE / Enolase superfamily enzyme
Function / homology
Function and homology information


mandelate racemase / mandelate racemase activity / mandelate catabolic process / amino acid catabolic process / hydro-lyase activity / metal 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
TARTRONATE / Mandelate racemase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLietzan, A.D. / St.Maurice, M.
CitationJournal: Biochemistry / Year: 2014
Title: Potent inhibition of mandelate racemase by a fluorinated substrate-product analogue with a novel binding mode.
Authors: Nagar, M. / Lietzan, A.D. / St Maurice, M. / Bearne, S.L.
History
DepositionAug 11, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2014Group: Database references
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Jan 31, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Sep 20, 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_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
B: Mandelate racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,8946
Polymers82,6092
Non-polymers2854
Water11,476637
1
A: Mandelate racemase
B: Mandelate racemase
hetero molecules

A: Mandelate racemase
B: Mandelate racemase
hetero molecules

A: Mandelate racemase
B: Mandelate racemase
hetero molecules

A: Mandelate racemase
B: Mandelate racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)331,57624
Polymers330,4378
Non-polymers1,13916
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
Buried area29600 Å2
ΔGint-234 kcal/mol
Surface area83400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.350, 149.350, 177.752
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-666-

HOH

21A-778-

HOH

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Components

#1: Protein Mandelate racemase / / MR


Mass: 41304.621 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: mdlA / Plasmid: pET-52b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P11444, mandelate racemase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-TTN / TARTRONATE


Mass: 118.045 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O5
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 637 / 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: 3 Å3/Da / Density % sol: 59 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 14% (w/v) PEG 1500, 100 mM glycine, 100 mM Triethanolamine (pH 8.5), VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 3, 2013
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 91291 / Num. obs: 90212 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 10.1 % / Biso Wilson estimate: 13.6 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 29.5
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 8.7 % / Rmerge(I) obs: 0.376 / Mean I/σ(I) obs: 5 / Num. unique all: 4535 / % possible all: 99.8

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Processing

Software
NameVersionClassification
MD2diffractometer software from EMBLdata collection
PHASERphasing
REFMAC5.7.0032refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2MNR

2mnr


Resolution: 1.8→32.38 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.639 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17073 4570 5 %RANDOM
Rwork0.14662 ---
obs0.14784 86721 98.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.043 Å2
Baniso -1Baniso -2Baniso -3
1--0.87 Å20 Å20 Å2
2---0.87 Å20 Å2
3---1.73 Å2
Refinement stepCycle: LAST / Resolution: 1.8→32.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5377 0 18 637 6032
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0195794
X-RAY DIFFRACTIONr_bond_other_d0.0010.025673
X-RAY DIFFRACTIONr_angle_refined_deg1.7541.9717931
X-RAY DIFFRACTIONr_angle_other_deg0.92313046
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.245774
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.06324.027221
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.00215941
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7061532
X-RAY DIFFRACTIONr_chiral_restr0.1220.2933
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0216613
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021251
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6161.8522992
X-RAY DIFFRACTIONr_mcbond_other1.6161.8512991
X-RAY DIFFRACTIONr_mcangle_it2.3832.7723749
X-RAY DIFFRACTIONr_mcangle_other2.3822.7733750
X-RAY DIFFRACTIONr_scbond_it2.1412.0312802
X-RAY DIFFRACTIONr_scbond_other2.1382.032799
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.182.9814163
X-RAY DIFFRACTIONr_long_range_B_refined4.92515.4026805
X-RAY DIFFRACTIONr_long_range_B_other4.55814.7396454
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 313 -
Rwork0.2 6393 -
obs-6393 99.23 %

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