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Entry
Database: PDB / ID: 3ops
TitleCrystal structure of mandelate racemase/muconate lactonizing protein FROM GEOBACILLUS SP. Y412MC10 complexed with magnesium/tartrate
ComponentsMandelate racemase/muconate lactonizing protein
KeywordsISOMERASE / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / NEW YORK STRUCTURAL GENOMIX RESEARCH CONSORTIUM / NYSGXRC / racemase / PSI-2 / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


hydro-lyase activity / metal ion binding
Similarity search - Function
: / 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 ...: / 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
D(-)-TARTARIC ACID / Mandelate racemase/muconate lactonizing protein
Similarity search - Component
Biological speciesGeobacillus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsMalashkevich, V.N. / Patskovsky, Y. / Ramagopal, U. / Toro, R. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure ofmandelate racemase/muconate lactonizing protein FROM GEOBACILLUS SP. Y412MC10 complexed with magnesium/tartrate
Authors: Malashkevich, V.N. / Patskovsky, Y. / Ramagopal, U. / Toro, R. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionSep 1, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 21, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.3Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_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.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.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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mandelate racemase/muconate lactonizing protein
B: Mandelate racemase/muconate lactonizing protein
C: Mandelate racemase/muconate lactonizing protein
D: Mandelate racemase/muconate lactonizing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,13817
Polymers177,1934
Non-polymers94513
Water16,844935
1
A: Mandelate racemase/muconate lactonizing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6475
Polymers44,2981
Non-polymers3494
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mandelate racemase/muconate lactonizing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4974
Polymers44,2981
Non-polymers1993
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Mandelate racemase/muconate lactonizing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4974
Polymers44,2981
Non-polymers1993
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Mandelate racemase/muconate lactonizing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4974
Polymers44,2981
Non-polymers1993
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Mandelate racemase/muconate lactonizing protein
hetero molecules

C: Mandelate racemase/muconate lactonizing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,1449
Polymers88,5972
Non-polymers5477
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_545x+1/2,y-1/2,z1
Buried area3580 Å2
ΔGint-43 kcal/mol
Surface area29950 Å2
MethodPISA
6
B: Mandelate racemase/muconate lactonizing protein
hetero molecules

D: Mandelate racemase/muconate lactonizing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,9948
Polymers88,5972
Non-polymers3976
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555x+1/2,y+1/2,z1
Buried area3110 Å2
ΔGint-46 kcal/mol
Surface area30760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.989, 66.375, 154.854
Angle α, β, γ (deg.)90.000, 96.590, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Mandelate racemase/muconate lactonizing protein


Mass: 44298.352 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus sp. (bacteria) / Strain: Y412MC10 / Gene: 192811615, GYMC10_3367 / Plasmid: BC-PSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CODON+RIL / References: UniProt: D3EID5
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-TAR / D(-)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H6O6
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 935 / 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: 2.3 Å3/Da / Density % sol: 46.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2 M MG CHLORIDE, 0.1 M TRIS-HCL, 25% PEG 3350, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 19, 2010
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 83601 / % possible obs: 77.6 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.13 / Χ2: 0.712 / Net I/σ(I): 3.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2-2.031.70.95928590.709154
2.03-2.071.80.9431090.671157.5
2.07-2.111.90.8733190.687162
2.11-2.1520.77635150.694165.3
2.15-2.22.10.75937870.717170.8
2.2-2.252.10.73940830.705176.8
2.25-2.312.20.69543260.697180.8
2.31-2.372.30.5845110.692183.5
2.37-2.442.40.5645840.683185.5
2.44-2.522.50.48245900.717185.7
2.52-2.612.50.43445940.733185.4
2.61-2.712.50.35246270.75186.1
2.71-2.842.50.28845660.747185
2.84-2.992.60.22945520.741184.3
2.99-3.172.60.16845570.769184.2
3.17-3.422.70.12544790.794183.1
3.42-3.762.80.08944880.809182.6
3.76-4.312.90.06644100.697181.3
4.31-5.4230.05343550.595179.8
5.42-403.20.04742900.609176.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3N4F

3n4f


Resolution: 2.2→20 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.872 / WRfactor Rfree: 0.2911 / WRfactor Rwork: 0.2138 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.743 / SU B: 22.947 / SU ML: 0.259 / SU R Cruickshank DPI: 0.5715 / SU Rfree: 0.3346 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.335 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3106 3428 5.1 %RANDOM
Rwork0.2279 ---
obs0.2321 67849 82.52 %-
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 max: 105.61 Å2 / Biso mean: 38.2209 Å2 / Biso min: 6.55 Å2
Baniso -1Baniso -2Baniso -3
1-0.38 Å20 Å2-0.3 Å2
2---0.35 Å20 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12094 0 58 935 13087
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02112474
X-RAY DIFFRACTIONr_angle_refined_deg1.2811.94316918
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.02351544
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.3423.573627
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.817152023
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7991598
X-RAY DIFFRACTIONr_chiral_restr0.0890.21789
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0219720
X-RAY DIFFRACTIONr_mcbond_it0.6533.57564
X-RAY DIFFRACTIONr_mcangle_it3.0415012056
X-RAY DIFFRACTIONr_scbond_it7.14504910
X-RAY DIFFRACTIONr_scangle_it0.5494.54855
LS refinement shellResolution: 2.2→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.38 223 -
Rwork0.289 4275 -
all-4498 -
obs--75.13 %
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)
10.3085-0.1435-0.00030.1668-0.05460.1673-0.0183-0.0732-0.02020.09910.0030.0775-0.003-0.02310.01530.0979-0.03630.08010.0524-0.030.067318.3954-30.37122.4677
20.53750.442-0.00610.45340.00140.2918-0.0074-0.14470.0726-0.0565-0.08150.08160.0191-0.00870.08890.05530.038-0.02540.1272-0.0450.048514.10151.600960.832
30.3064-0.2460.03580.43460.07170.13740.02410.04680.04360.0782-0.059-0.04970.02730.00340.0350.0443-0.0177-0.01150.04250.02180.0221-21.65050.846114.8213
40.48220.25060.37190.27580.27110.33410.03280.0944-0.0377-0.1210.0071-0.0847-0.04340.0707-0.03990.14010.09680.08260.15290.08010.0677-26.1331-29.12156.1443
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999
3X-RAY DIFFRACTION3C-10 - 9999
4X-RAY DIFFRACTION4D-10 - 9999

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