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- PDB-4h83: Crystal structure of Mandelate racemase/muconate lactonizing enzy... -

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Basic information

Entry
Database: PDB / ID: 4h83
TitleCrystal structure of Mandelate racemase/muconate lactonizing enzyme (EFI target:502127)
ComponentsMandelate racemase/muconate lactonizing enzyme
KeywordsISOMERASE / Structural Genomics / Enzyme Function Initiative / Tim Barrel / racemase/enolase
Function / homology
Function and homology information


hydro-lyase activity / metal ion binding
Similarity search - Function
: / 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 ...: / 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
BICARBONATE ION / PHOSPHATE ION / Mandelate racemase/muconate lactonizing enzyme
Similarity search - Component
Biological speciesmarine actinobacterium PHSC20C1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.094 Å
AuthorsKim, J. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Washington, E. / Scott Glenn, A. / Chowdhury, S. ...Kim, J. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Stead, M. / Hillerich, B. / Love, J. / Seidel, R.D. / Imker, H.J. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
CitationJournal: To be Published
Title: Crystal structure of Mandelate racemase/muconate lactonizing enzyme
Authors: Kim, J. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Stead, M. / ...Authors: Kim, J. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Stead, M. / Hillerich, B. / Love, J. / Seidel, R.D. / Imker, H.J. / Gerlt, J.A. / Almo, S.C.
History
DepositionSep 21, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2012Group: Structure summary
Revision 1.2Sep 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_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_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.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_conn.ptnr2_label_seq_id / _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
C: Mandelate racemase/muconate lactonizing enzyme
D: Mandelate racemase/muconate lactonizing enzyme
E: Mandelate racemase/muconate lactonizing enzyme
F: Mandelate racemase/muconate lactonizing enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)261,44418
Polymers260,9516
Non-polymers49312
Water15,619867
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20620 Å2
ΔGint-128 kcal/mol
Surface area65750 Å2
MethodPISA
2
A: Mandelate racemase/muconate lactonizing enzyme
B: Mandelate racemase/muconate lactonizing enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,1377
Polymers86,9842
Non-polymers1535
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2670 Å2
ΔGint-33 kcal/mol
Surface area25670 Å2
MethodPISA
3
C: Mandelate racemase/muconate lactonizing enzyme
D: Mandelate racemase/muconate lactonizing enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,1255
Polymers86,9842
Non-polymers1413
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2650 Å2
ΔGint-36 kcal/mol
Surface area26470 Å2
MethodPISA
4
E: Mandelate racemase/muconate lactonizing enzyme
F: Mandelate racemase/muconate lactonizing enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,1836
Polymers86,9842
Non-polymers1994
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2860 Å2
ΔGint-40 kcal/mol
Surface area25800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.983, 102.950, 234.431
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsTHE AUTHOR STATES THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Mandelate racemase/muconate lactonizing enzyme


Mass: 43491.840 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) marine actinobacterium PHSC20C1 (bacteria)
Strain: PHSC20C1 / Gene: A20C1_08358 / Production host: Escherichia coli (E. coli) / References: UniProt: A4AFX2

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Non-polymers , 5 types, 879 molecules

#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-BCT / BICARBONATE ION / Bicarbonate


Mass: 61.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 867 / 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: 2.08 Å3/Da / Density % sol: 40.88 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Sodium Citrate, 20% (w/v) PEG 4000, 5% (v/v) 2-Propanol, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 27, 2012
RadiationMonochromator: Double silicon(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 113134 / % possible obs: 87.9 % / Redundancy: 10.5 % / Biso Wilson estimate: 23.77 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 24
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 10.5 % / Rmerge(I) obs: 0.92 / Mean I/σ(I) obs: 2.5 / % possible all: 78.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
CBASSdata collection
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NO1

3no1


Resolution: 2.094→47.131 Å / Occupancy max: 1 / Occupancy min: 0.34 / FOM work R set: 0.8621 / SU ML: 0.21 / σ(F): 1.34 / Phase error: 20.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2044 5358 5 %random
Rwork0.1473 ---
obs0.1501 107240 83.33 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 129.15 Å2 / Biso mean: 28.849 Å2 / Biso min: 8.68 Å2
Refinement stepCycle: LAST / Resolution: 2.094→47.131 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16810 0 27 867 17704
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01217298
X-RAY DIFFRACTIONf_angle_d1.34923578
X-RAY DIFFRACTIONf_chiral_restr0.0782545
X-RAY DIFFRACTIONf_plane_restr0.0073061
X-RAY DIFFRACTIONf_dihedral_angle_d14.2086153
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0937-2.11750.2112860.14881762184844
2.1175-2.14240.23821280.14722118224652
2.1424-2.16850.21311300.15232408253860
2.1685-2.1960.25141440.15372526267063
2.196-2.22490.2621400.15692773291369
2.2249-2.25530.21791390.15442817295670
2.2553-2.28760.23241640.16062944310873
2.2876-2.32170.23511430.15323029317274
2.3217-2.3580.20961600.1593092325277
2.358-2.39660.24541660.15743182334879
2.3966-2.4380.271660.14993220338679
2.438-2.48230.23091770.14783211338880
2.4823-2.530.21761740.15743258343281
2.53-2.58170.19851820.15983336351882
2.5817-2.63780.2271600.16113400356083
2.6378-2.69920.25782010.1643378357985
2.6992-2.76660.22731690.16333518368786
2.7666-2.84140.231980.15993582378088
2.8414-2.9250.22491810.15753735391691
2.925-3.01940.20242120.16083755396793
3.0194-3.12730.23072150.15873909412496
3.1273-3.25250.19982050.16223985419098
3.2525-3.40050.19132060.1464013421998
3.4005-3.57970.18862260.14614010423698
3.5797-3.80390.19372540.13834020427499
3.8039-4.09750.16571980.1264088428699
4.0975-4.50950.16441800.11564146432699
4.5095-5.16140.15732090.11874116432599
5.1614-6.50010.212070.1564205441299
6.5001-47.14250.20952380.162543464584100

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