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- PDB-4e8g: Crystal structure of an enolase (mandelate racemase subgroup) fro... -

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Basic information

Entry
Database: PDB / ID: 4e8g
TitleCrystal structure of an enolase (mandelate racemase subgroup) from paracococus denitrificans pd1222 (target nysgrc-012907) with bound mg
ComponentsMandelate racemase/muconate lactonizing enzyme, N-terminal domain protein
KeywordsISOMERASE / Putative Racemase / 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 / amino-acid racemase activity / 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
Unknown ligand / 4-hydroxyproline betaine 2-epimerase
Similarity search - Component
Biological speciesParacoccus denitrificans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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. / Zencheck, W.D. / 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
DepositionMar 20, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2012Provider: 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 1.2Sep 13, 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _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
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)84,6996
Polymers84,6262
Non-polymers734
Water8,575476
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)338,79524
Polymers338,5048
Non-polymers29216
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 area31980 Å2
ΔGint-194 kcal/mol
Surface area81040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.963, 117.963, 111.154
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Detailsbiological unit is an octamer

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Components

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


Mass: 42312.949 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paracoccus denitrificans (bacteria) / Strain: PD1222 / Gene: Pden_1187 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A1B198
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 476 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 46.16 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Protein (10 mM Hepes, pH 7.8, 150 mM NaCl, 10% glycerol, 5 mM MgCl); Reservoir (0.1 M Magnesium Chloride 0.1 M MES:NaOH pH 6.5 30% (v/v) PEG 400); Cryoprotection (Reservoir), sitting drop ...Details: Protein (10 mM Hepes, pH 7.8, 150 mM NaCl, 10% glycerol, 5 mM MgCl); Reservoir (0.1 M Magnesium Chloride 0.1 M MES:NaOH pH 6.5 30% (v/v) PEG 400); Cryoprotection (Reservoir), sitting drop vapor diffuction, 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: Mar 12, 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: 2→117.963 Å / Num. all: 53519 / Num. obs: 53519 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.1 % / Rmerge(I) obs: 0.116 / Rsym value: 0.116 / Net I/σ(I): 16.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2-2.1113.30.7071.110188876880.707100
2.11-2.24140.4861.510157672720.486100
2.24-2.3914.40.3132.49907868760.313100
2.39-2.5814.60.233.29357764120.23100
2.58-2.8314.60.164.68655959100.16100
2.83-3.1614.50.1126.67825953800.112100
3.16-3.6514.30.088.96831047800.08100
3.65-4.4713.90.06110.95686540930.061100
4.47-6.3213.80.055124438932170.055100
6.32-117.96312.60.0513.72383218910.0599.6

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHENIX1.7.3_928refinement
PDB_EXTRACT3.1data extraction
MOSFLMdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2PMQ

2pmq


Resolution: 2→55.577 Å / Occupancy max: 1 / Occupancy min: 0.41 / FOM work R set: 0.8672 / SU ML: 0.17 / σ(F): 1.34 / σ(I): 0 / Phase error: 19.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.202 2713 5.07 %RANDOM
Rwork0.1627 ---
all0.1647 53463 --
obs0.1647 53463 99.93 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Bsol: 41.365 Å2 / ksol: 0.352 e/Å3
Displacement parametersBiso max: 110.01 Å2 / Biso mean: 28.5934 Å2 / Biso min: 9.76 Å2
Baniso -1Baniso -2Baniso -3
1--1.9847 Å2-0 Å20 Å2
2---1.9847 Å20 Å2
3---3.9693 Å2
Refinement stepCycle: LAST / Resolution: 2→55.577 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5413 0 8 476 5897
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085593
X-RAY DIFFRACTIONf_angle_d1.0837626
X-RAY DIFFRACTIONf_chiral_restr0.067839
X-RAY DIFFRACTIONf_plane_restr0.0051011
X-RAY DIFFRACTIONf_dihedral_angle_d13.3072068
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.03640.26371420.214826082750100
2.0364-2.07560.25861310.188126412772100
2.0756-2.11790.20641460.17626192765100
2.1179-2.1640.261170.177426492766100
2.164-2.21430.2531560.171126232779100
2.2143-2.26970.26061480.166626452793100
2.2697-2.33110.22571370.162726532790100
2.3311-2.39970.21351600.157826062766100
2.3997-2.47710.27091330.169226432776100
2.4771-2.56560.22791490.166126672816100
2.5656-2.66840.21521560.155726212777100
2.6684-2.78980.22141330.164226692802100
2.7898-2.93690.20461400.163626742814100
2.9369-3.12090.19381340.168526812815100
3.1209-3.36180.20381470.165526732820100
3.3618-3.70010.20551200.155827432863100
3.7001-4.23530.15081350.140227062841100
4.2353-5.33540.15321710.143527382909100
5.3354-55.59840.19341580.18022891304999
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)
12.13530.6074-0.26411.86541.27451.21140.07710.03270.2384-0.09140.1344-0.4427-0.3210.0172-0.06530.08650.0161-0.01730.1362-0.02510.213841.61855.561920.6817
21.0623-0.44590.10681.6509-0.32751.05190.08580.09410.0903-0.0493-0.0058-0.1178-0.10360.0406-0.08290.102-0.00340.01120.1207-0.00970.119319.079460.39552.642
30.7426-0.2260.25050.94310.40381.06170.05210.07670.0821-0.08380.0389-0.3052-0.07840.1544-0.06710.09580.01370.03280.1209-0.01380.202436.206650.553611.7829
40.84290.4250.61592.29030.0561.56720.062-0.0816-0.1484-0.0341-0.00330.00370.1283-0.1824-0.05040.16370.0176-0.03320.1703-0.00130.196226.023125.273126.3137
51.6175-0.0718-0.02850.961-0.02560.97830.0414-0.1366-0.1890.09530.04330.04110.0368-0.084-0.07650.1365-0.0008-0.01890.14810.03380.08048.718442.054146.391
60.5072-0.20540.16540.90120.1170.9076-0.0118-0.0888-0.13760.13580.0384-0.1040.11170.0097-0.03980.18890.0222-0.05520.1870.03780.180226.164331.880637.5538
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resseq 1:130)B1 - 130
2X-RAY DIFFRACTION2chain 'B' and (resseq 131:261)B131 - 261
3X-RAY DIFFRACTION3chain 'B' and (resseq 262:369)B262 - 369
4X-RAY DIFFRACTION4chain 'A' and (resseq 1:130)A1 - 130
5X-RAY DIFFRACTION5chain 'A' and (resseq 131:261)A131 - 261
6X-RAY DIFFRACTION6chain 'A' and (resseq 262:369)A262 - 369

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