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

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Basic information

Entry
Database: PDB / ID: 4izg
TitleCrystal structure of an enolase (mandelate racemase subgroup) from paracococus denitrificans pd1222 (target nysgrc-012907) with bound cis-4oh-d-proline betaine (product)
ComponentsMandelate racemase/muconate lactonizing enzyme, N-terminal domain protein
KeywordsISOMERASE / Enolase / Betaine Racemase / Proline Betaine Racemease / NYSGRC / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium
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
Chem-4OP / IODIDE ION / 4-hydroxyproline betaine 2-epimerase
Similarity search - Component
Biological speciesParacoccus denitrificans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.7 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
DepositionJan 29, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 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)87,83836
Polymers83,9692
Non-polymers3,86834
Water14,178787
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)351,351144
Polymers335,8788
Non-polymers15,473136
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 area48740 Å2
ΔGint-155 kcal/mol
Surface area77880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.463, 117.463, 111.049
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
11A-857-

HOH

21B-740-

HOH

31B-757-

HOH

Detailsbiological unit is an octamer

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Components

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


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
#2: Chemical...
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: I
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-4OP / (2S,4S)-2-carboxy-4-hydroxy-1,1-dimethylpyrrolidinium / CIS-4OH-D-PROLINE BETAINE


Type: D-peptide linking / Mass: 160.191 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H14NO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 787 / 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: 46.07 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Protein (10 mM Hepes pH 7.8, 150 mM NaCl, 5% glycerol, 1 mM EDTA/DTT); Reservoir (30% Peg300, MES pH 7.0, 200 mM MgCl); Cryoprotection (Reservoir+250 mM trans-4OH-L-Proline Betaine, comes ...Details: Protein (10 mM Hepes pH 7.8, 150 mM NaCl, 5% glycerol, 1 mM EDTA/DTT); Reservoir (30% Peg300, MES pH 7.0, 200 mM MgCl); Cryoprotection (Reservoir+250 mM trans-4OH-L-Proline Betaine, comes with approx equal molar of iodine during synthesis of trans-4OH-L-Proline Betaine), 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: Jul 9, 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: 1.7→111.049 Å / Num. all: 85566 / Num. obs: 85566 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.8 % / Rmerge(I) obs: 0.104 / Rsym value: 0.104 / Net I/σ(I): 15.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.7-1.798.30.7731102128122780.77399.8
1.79-1.99.50.541.4111281116900.5499.9
1.9-2.0310.80.3532.1118855109800.35399.9
2.03-2.19120.2373.1123052102540.237100
2.19-2.4130.1714.312325294840.171100
2.4-2.6913.80.1335.411906086130.133100
2.69-3.114.10.0977.210804376510.097100
3.1-3.814.10.06110.99187665050.061100
3.8-5.38140.043157192651290.043100
5.38-117.46313.40.03319.63986729820.03399.9

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
MOSFLMdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.7→80.696 Å / Occupancy max: 1 / Occupancy min: 0.29 / FOM work R set: 0.8664 / SU ML: 0.16 / σ(F): 0 / σ(I): 0 / Phase error: 19.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1966 4275 5 %RANDOM
Rwork0.1653 ---
all0.1668 85473 --
obs0.1668 85473 99.82 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 73.08 Å2 / Biso mean: 16.388 Å2 / Biso min: 3.19 Å2
Refinement stepCycle: LAST / Resolution: 1.7→80.696 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5538 0 54 787 6379
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085727
X-RAY DIFFRACTIONf_angle_d1.1037821
X-RAY DIFFRACTIONf_chiral_restr0.068858
X-RAY DIFFRACTIONf_plane_restr0.0061030
X-RAY DIFFRACTIONf_dihedral_angle_d13.0332133
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 (%)
1.7-1.71930.31641350.240826652800100
1.7193-1.73960.27071210.223126872808100
1.7396-1.76080.24691370.213626592796100
1.7608-1.78310.24121330.210126742807100
1.7831-1.80650.22321310.198626722803100
1.8065-1.83130.21971260.18726732799100
1.8313-1.85740.26261530.18826622815100
1.8574-1.88520.21881520.184726692821100
1.8852-1.91460.21121210.1826852806100
1.9146-1.9460.24471400.176526942834100
1.946-1.97960.20941410.178926752816100
1.9796-2.01560.20741400.168226542794100
2.0156-2.05440.21361750.16626702845100
2.0544-2.09630.21131210.160727222843100
2.0963-2.14190.20371480.166726502798100
2.1419-2.19170.18911570.152526832840100
2.1917-2.24650.21531610.15826792840100
2.2465-2.30730.19521310.154627072838100
2.3073-2.37520.1961360.154526952831100
2.3752-2.45180.19671500.162626972847100
2.4518-2.53950.19461450.16526932838100
2.5395-2.64110.17621300.155727282858100
2.6411-2.76130.19771510.167826992850100
2.7613-2.90690.22281620.169927062868100
2.9069-3.08910.18591330.167327562889100
3.0891-3.32760.18641430.153327402883100
3.3276-3.66250.1641410.148727572898100
3.6625-4.19240.15871460.141427872933100
4.1924-5.28190.15211440.144628132957100
5.2819-80.78680.2011710.18372947311899
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)
10.18610.08280.17130.22550.05670.15480.0333-0.0558-0.07690.0107-0.0234-0.01260.01-0.029900.05110.0052-0.01410.0592-0.00150.07624.147824.752628.8569
20.19930.00390.1250.0010.00760.14230.0489-0.0421-0.07670.02810.00740.01060.0293-0.03040.14660.0822-0.015-0.03930.11120.04060.035711.301338.129953.1877
30.0828-0.0215-0.02560.10630.02190.0650.0106-0.0176-0.0210.01350.0049-0.05530.00660.01030.01070.04150.013-0.05060.03960.0079-0.014618.526136.841337.9948
40.1587-0.0007-0.08640.25490.21330.21450.0403-0.00260.0369-0.04010.0522-0.1507-0.04240.02890.03530.05450.00250.00460.0616-0.02730.115441.22955.104919.9583
50.03170.02710.07110.41650.11730.17230.03790.06980.043-0.03220.0143-0.0836-0.0103-0.00540.06390.08220.01470.03580.07190.00630.055622.953859.8332-5.6476
60.02640.0068-0.00710.0408-0.02040.01050.0069-0.01080.03420.02070.03120.0054-0.0172-0.0175-00.06860.0031-0.00190.067-0.00850.04414.427761.223910.5263
70.0743-0.055-0.02250.07130.07420.10.0407-0.00680.0049-0.02180.0329-0.1320.01010.01480.02720.05020.00540.02180.0642-0.02240.10836.518750.336111.6458
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 130 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 131 through 200 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 201 through 369 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 133 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 134 through 194 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 195 through 261 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 262 through 369 )B0

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