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- PDB-4j1o: Crystal structure of an enolase (mandelate racemase subgroup) fro... -

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Basic information

Entry
Database: PDB / ID: 4j1o
TitleCrystal structure of an enolase (mandelate racemase subgroup) from paracococus denitrificans pd1222 (target nysgrc-012907) with bound l-proline betaine (substrate)
ComponentsMandelate racemase/muconate lactonizing enzyme, N-terminal domain protein
KeywordsISOMERASE / Enolase / Betaine Racemase / Proline Betaine Racemease / NYSGRC / Structural Genomics / New York Structural Genomics Research Consortium / PSI-Biology
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 / metal 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
IODIDE ION / 1,1-DIMETHYL-PROLINIUM / 4-hydroxyproline betaine 2-epimerase
Similarity search - Component
Biological speciesParacoccus denitrificans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.6 Å
AuthorsVetting, M.W. / Toro, R. / Bhosle, R. / Wasserman, S.R. / Morisco, L.L. / Sojitra, S. / Chamala, S. / Kar, A. / LaFleur, J. / Villigas, G. ...Vetting, M.W. / Toro, R. / Bhosle, R. / Wasserman, S.R. / Morisco, L.L. / Sojitra, S. / Chamala, S. / Kar, A. / LaFleur, J. / Villigas, G. / Evans, B. / Hammonds, J. / Gizzi, A. / Stead, M. / Hillerich, B. / Love, J. / Seidel, R.D. / Bonanno, J.B. / Gerlt, J.A. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: MBio / Year: 2014
Title: Prediction and biochemical demonstration of a catabolic pathway for the osmoprotectant proline betaine.
Authors: Kumar, R. / Zhao, S. / Vetting, M.W. / Wood, B.M. / Sakai, A. / Cho, K. / Solbiati, J. / Almo, S.C. / Sweedler, J.V. / Jacobson, M.P. / Gerlt, J.A. / Cronan, J.E.
History
DepositionFeb 1, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 28, 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_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_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, N-terminal domain protein
B: Mandelate racemase/muconate lactonizing enzyme, N-terminal domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,86721
Polymers83,9692
Non-polymers1,89819
Water12,412689
1
A: Mandelate racemase/muconate lactonizing enzyme, N-terminal domain protein
B: Mandelate racemase/muconate lactonizing enzyme, N-terminal domain protein
hetero molecules

A: Mandelate racemase/muconate lactonizing enzyme, N-terminal domain protein
B: Mandelate racemase/muconate lactonizing enzyme, N-terminal domain protein
hetero molecules

A: Mandelate racemase/muconate lactonizing enzyme, N-terminal domain protein
B: Mandelate racemase/muconate lactonizing enzyme, N-terminal domain protein
hetero molecules

A: Mandelate racemase/muconate lactonizing enzyme, N-terminal domain protein
B: Mandelate racemase/muconate lactonizing enzyme, N-terminal domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)343,46984
Polymers335,8788
Non-polymers7,59276
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-y+1/2,x+1/2,z1
crystal symmetry operation4_455y-1/2,-x+1/2,z1
Buried area39090 Å2
ΔGint-163 kcal/mol
Surface area78970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.297, 117.297, 110.528
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11B-732-

HOH

21B-775-

HOH

Detailsbiological unit is an octamer

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Mandelate racemase/muconate lactonizing enzyme, N-terminal domain protein


Mass: 41984.688 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paracoccus denitrificans (bacteria) / Strain: PD1222 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A1B198

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Non-polymers , 5 types, 708 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: I
#4: 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
#5: Chemical ChemComp-PBE / 1,1-DIMETHYL-PROLINIUM / PROLINE BETAINE


Mass: 144.192 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H14NO2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 689 / 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: 2.26 Å3/Da / Density % sol: 45.67 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.7
Details: Protein (10 mM Hepes pH 7.8, 150 mM NaCl, 5% glycerol, 1 mM EDTA/DTT); Reservoir (20% Peg400, 200 mM MgCl2, 100 mM MES pH 6.7); Cryoprotection (Reservoir+200 mM L-Proline Betaine+ 20% ...Details: Protein (10 mM Hepes pH 7.8, 150 mM NaCl, 5% glycerol, 1 mM EDTA/DTT); Reservoir (20% Peg400, 200 mM MgCl2, 100 mM MES pH 6.7); Cryoprotection (Reservoir+200 mM L-Proline Betaine+ 20% glycerol, comes with approx equal molar of iodine during synthesis of L-Proline Betaine), sitting drop vapor diffusion, temperature 298K, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Apr 14, 2012 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.6→110.528 Å / Num. all: 101674 / Num. obs: 101674 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13 % / Rmerge(I) obs: 0.107 / Rsym value: 0.107 / Net I/σ(I): 16.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.6-1.6910.70.61.3156913146360.6100
1.69-1.7911.70.4411.7162068138830.441100
1.79-1.9112.60.3092.5165571130920.309100
1.91-2.0713.50.2123.5164273121910.212100
2.07-2.26140.1534.9157978112560.153100
2.26-2.5314.30.1196.2145804102190.119100
2.53-2.9214.30.0937.712960490650.093100
2.92-3.5814.10.0691010885877330.069100
3.58-5.0613.80.0513.28369060720.05100
5.06-117.29713.40.04115.34719535270.04199.9

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
MOSFLMdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.6→37.093 Å / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.9002 / SU ML: 0.12 / σ(F): 0 / σ(I): 0 / Phase error: 16.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1809 5074 4.99 %RANDOM
Rwork0.1575 ---
all0.1586 101606 --
obs0.1586 101606 99.96 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 67.41 Å2 / Biso mean: 15.238 Å2 / Biso min: 4.43 Å2
Refinement stepCycle: LAST / Resolution: 1.6→37.093 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5538 0 42 689 6269
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075882
X-RAY DIFFRACTIONf_angle_d1.1218055
X-RAY DIFFRACTIONf_chiral_restr0.071877
X-RAY DIFFRACTIONf_plane_restr0.0061069
X-RAY DIFFRACTIONf_dihedral_angle_d16.3472207
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.6-1.61820.22161600.197831733333
1.6182-1.63720.21941540.190431653319
1.6372-1.65720.21710.176531973368
1.6572-1.67820.22311830.182231423325
1.6782-1.70030.20561560.175332063362
1.7003-1.72350.21391590.16831683327
1.7235-1.74820.2021820.169631943376
1.7482-1.77430.21361600.170631653325
1.7743-1.8020.19271660.168731723338
1.802-1.83150.18381780.158631913369
1.8315-1.86310.1881620.155832023364
1.8631-1.8970.20051660.157931923358
1.897-1.93350.18611570.153931913348
1.9335-1.97290.19261570.157632023359
1.9729-2.01580.19571710.158132083379
2.0158-2.06270.18571700.155631773347
2.0627-2.11430.19181660.151131803346
2.1143-2.17150.15861640.149432403404
2.1715-2.23530.17491820.1531843366
2.2353-2.30750.1711600.1532213381
2.3075-2.38990.17291860.148231803366
2.3899-2.48560.17231850.155332103395
2.4856-2.59870.19091450.153932483393
2.5987-2.73570.17771980.155932083406
2.7357-2.9070.19821630.161232533416
2.907-3.13140.19341740.1632503424
3.1314-3.44630.18021570.152932913448
3.4463-3.94450.17021850.139732883473
3.9445-4.96770.13571930.139833143507
4.9677-37.10250.18281640.183835203684
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.39160.07790.63632.4551-0.23710.94380.011-0.3989-0.1960.3526-0.01910.16180.1108-0.21520.04950.1385-0.0079-0.03570.17070.02730.138920.34419.535135.7686
20.86430.42320.43420.99910.18370.78620.0109-0.0192-0.077-0.0515-0.0009-0.05850.00730.0016-0.01040.0650.0236-0.0080.059-0.00740.062326.190727.339125.5717
32.4179-0.2936-0.05280.8072-0.24091.56560.0173-0.1692-0.17850.12390.05770.0060.0842-0.07-0.05960.09750.0013-0.02230.07750.02240.048712.243638.429554.0592
40.4838-0.1384-0.17210.26060.10670.28120.0017-0.0371-0.0480.02560.0092-0.01480.04120.0222-0.0130.06230.0062-0.02010.06050.00240.03817.855436.80337.8698
52.1618-0.1953-0.37541.46061.04090.7680.10280.24520.0721-0.30610.0393-0.2533-0.16530.0563-0.08370.1013-0.02060.04040.1011-0.04730.150443.060760.963717.0422
60.4887-0.18570.08180.45270.0190.35370.03160.03730.0283-0.0489-0.0021-0.0897-0.00250.045-0.01760.0422-0.00330.01930.0458-0.01220.053129.063254.27049.8816
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 1:39)A1 - 39
2X-RAY DIFFRACTION2chain 'A' and (resseq 40:130)A40 - 130
3X-RAY DIFFRACTION3chain 'A' and (resseq 131:194)A131 - 194
4X-RAY DIFFRACTION4chain 'A' and (resseq 195:369)A195 - 369
5X-RAY DIFFRACTION5chain 'B' and (resseq 1:75)B1 - 75
6X-RAY DIFFRACTION6chain 'B' and (resseq 76:369)B76 - 369

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