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- PDB-2pmq: Crystal structure of a mandelate racemase/muconate lactonizing en... -

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Basic information

Entry
Database: PDB / ID: 2pmq
TitleCrystal structure of a mandelate racemase/muconate lactonizing enzyme from Roseovarius sp. HTCC2601
ComponentsMandelate racemase/muconate lactonizing enzyme
KeywordsISOMERASE / Structural genomics / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


4-hydroxyproline betaine 2-epimerase / amino-acid betaine catabolic process / racemase activity, acting on amino acids and derivatives / racemase and epimerase activity, acting on amino acids and derivatives / magnesium ion binding
Similarity search - Function
4R-hydroxyproline betaine 2-epimerase / Mandelate racemase DgoD-like / 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 ...4R-hydroxyproline betaine 2-epimerase / Mandelate racemase DgoD-like / 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
4-hydroxyproline betaine 2-epimerase
Similarity search - Component
Biological speciesRoseovarius sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.72 Å
AuthorsBonanno, J.B. / Rutter, M. / Bain, K.T. / Lau, C. / Sridhar, V. / Smith, D. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: Nature / Year: 2013
Title: Discovery of new enzymes and metabolic pathways by using structure and genome context.
Authors: Zhao, S. / Kumar, R. / Sakai, A. / Vetting, M.W. / Wood, B.M. / Brown, S. / Bonanno, J.B. / Hillerich, B.S. / Seidel, R.D. / Babbitt, P.C. / Almo, S.C. / Sweedler, J.V. / Gerlt, J.A. / ...Authors: Zhao, S. / Kumar, R. / Sakai, A. / Vetting, M.W. / Wood, B.M. / Brown, S. / Bonanno, J.B. / Hillerich, B.S. / Seidel, R.D. / Babbitt, P.C. / Almo, S.C. / Sweedler, J.V. / Gerlt, J.A. / Cronan, J.E. / Jacobson, M.P.
History
DepositionApr 23, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Oct 24, 2012Group: Structure summary
Revision 1.4Sep 18, 2013Group: Database references
Revision 1.5Oct 30, 2013Group: Database references
Revision 1.6Nov 6, 2013Group: Database references
Revision 1.7Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.8Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.9Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / pdbx_struct_conn_angle ...audit_author / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _pdbx_struct_conn_angle.ptnr1_auth_asym_id ..._audit_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.ptnr1_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.ptnr1_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.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/muconate lactonizing enzyme
B: Mandelate racemase/muconate lactonizing enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,5047
Polymers82,3832
Non-polymers1225
Water12,376687
1
A: Mandelate racemase/muconate lactonizing enzyme
B: Mandelate racemase/muconate lactonizing enzyme
hetero molecules

A: Mandelate racemase/muconate lactonizing enzyme
B: Mandelate racemase/muconate lactonizing enzyme
hetero molecules

A: Mandelate racemase/muconate lactonizing enzyme
B: Mandelate racemase/muconate lactonizing enzyme
hetero molecules

A: Mandelate racemase/muconate lactonizing enzyme
B: Mandelate racemase/muconate lactonizing enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)330,01728
Polymers329,5318
Non-polymers48620
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_545-y+1/2,x-1/2,z1
crystal symmetry operation4_555y+1/2,-x+1/2,z1
Buried area30250 Å2
ΔGint-228 kcal/mol
Surface area85830 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)136.381, 136.381, 80.925
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-903-

MG

21B-905-

MG

31A-945-

HOH

41A-985-

HOH

51A-1118-

HOH

61A-1204-

HOH

71A-1235-

HOH

81B-963-

HOH

91B-1134-

HOH

101B-1197-

HOH

111B-1228-

HOH

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Components

#1: Protein Mandelate racemase/muconate lactonizing enzyme


Mass: 41191.375 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Roseovarius sp. (bacteria) / Strain: HTCC2601 / Gene: R2601_01638 / Plasmid: modified pET26 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q0FPQ4
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 687 / 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: 2.28 Å3/Da / Density % sol: 46.11 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 8.5
Details: 100mM Tris-HCl pH 8.5, 25% PEG 3350, 200mM Magnesium chloride, VAPOR DIFFUSION, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97958 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 8, 2007
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97958 Å / Relative weight: 1
ReflectionResolution: 1.72→96.436 Å / Num. all: 81085 / Num. obs: 81085 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12 % / Biso Wilson estimate: 17.8 Å2 / Rmerge(I) obs: 0.086 / Rsym value: 0.086 / Net I/σ(I): 22.2
Reflection shellResolution: 1.72→1.81 Å / Redundancy: 10.9 % / Rmerge(I) obs: 0.306 / Mean I/σ(I) obs: 6.1 / Num. unique all: 10981 / Rsym value: 0.306 / % possible all: 93

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
MAR345CCDdata collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHELXCDphasing
SHELXDphasing
SHELXEmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.72→20 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.819 / SU ML: 0.061 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.102 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.191 4061 5 %RANDOM
Rwork0.165 ---
obs0.167 81006 99.7 %-
all-81006 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 15.922 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2--0.02 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.72→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5626 0 5 687 6318
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0215870
X-RAY DIFFRACTIONr_bond_other_d0.0020.023923
X-RAY DIFFRACTIONr_angle_refined_deg1.3411.9538017
X-RAY DIFFRACTIONr_angle_other_deg0.90239547
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4835769
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.60623.113257
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.73515912
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7821546
X-RAY DIFFRACTIONr_chiral_restr0.0810.2889
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026689
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021210
X-RAY DIFFRACTIONr_nbd_refined0.2220.21209
X-RAY DIFFRACTIONr_nbd_other0.2040.24133
X-RAY DIFFRACTIONr_nbtor_refined0.1770.22866
X-RAY DIFFRACTIONr_nbtor_other0.0860.23022
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2487
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3150.227
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3560.277
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.160.266
X-RAY DIFFRACTIONr_mcbond_it1.1541.54482
X-RAY DIFFRACTIONr_mcbond_other0.221.51529
X-RAY DIFFRACTIONr_mcangle_it1.33825963
X-RAY DIFFRACTIONr_scbond_it2.36432398
X-RAY DIFFRACTIONr_scangle_it3.3194.52040
LS refinement shellResolution: 1.72→1.76 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.233 293 -
Rwork0.185 5416 -
obs-5709 96.52 %

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