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- PDB-3n4f: CRYSTAL STRUCTURE OF Mandelate racemase/muconate lactonizing prot... -

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Basic information

Entry
Database: PDB / ID: 3n4f
TitleCRYSTAL STRUCTURE OF Mandelate racemase/muconate lactonizing protein from Geobacillus sp. Y412MC10
ComponentsMandelate racemase/muconate lactonizing protein
KeywordsISOMERASE / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / NEW YORK STRUCTURAL GENOMIX RESEARCH CONSORTIUM / NYSGXRC / enolase / PSI-2 / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


hydro-lyase activity / carbohydrate catabolic process / magnesium 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
Mandelate racemase/muconate lactonizing protein
Similarity search - Component
Biological speciesGeobacillus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.88 Å
AuthorsMalashkevich, V.N. / 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 OF Mandelate racemase/muconate lactonizing protein from Geobacillus sp. Y412MC10
Authors: Malashkevich, V.N. / Toro, R. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionMay 21, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Nov 21, 2018Group: Data collection / Derived calculations / Structure summary
Category: audit_author / pdbx_struct_special_symmetry / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 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

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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)177,38812
Polymers177,1934
Non-polymers1948
Water25,3831409
1
A: Mandelate racemase/muconate lactonizing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3473
Polymers44,2981
Non-polymers492
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mandelate racemase/muconate lactonizing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3473
Polymers44,2981
Non-polymers492
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Mandelate racemase/muconate lactonizing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3473
Polymers44,2981
Non-polymers492
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Mandelate racemase/muconate lactonizing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3473
Polymers44,2981
Non-polymers492
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)155.387, 66.100, 151.536
Angle α, β, γ (deg.)90.00, 94.33, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11D-376-

TYR

Detailsmonomer

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1409 / 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: 2.19 Å3/Da / Density % sol: 43.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M Mg chloride, 0.1 M Tris-HCl, 25% PEG 3350, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 29, 2010
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionRedundancy: 2.8 % / Av σ(I) over netI: 11.73 / Number: 630082 / Rmerge(I) obs: 0.128 / Χ2: 1.76 / D res high: 1.88 Å / D res low: 50 Å / Num. obs: 227793 / % possible obs: 93.1
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.15099.310.0522.6282.9
4.055.199.110.0552.9542.7
3.544.059910.0673.0182.8
3.213.5498.110.082.6322.8
2.983.2197.410.0962.1372.8
2.812.9896.610.1151.8952.8
2.672.819610.1331.7142.8
2.552.6795.110.1561.5352.8
2.452.5594.710.1791.4262.8
2.372.4593.610.2061.3842.8
2.292.3792.410.231.3592.8
2.232.2991.810.2561.2952.8
2.172.2391.110.281.3092.8
2.122.1790.410.3161.2912.8
2.072.1289.610.3561.2822.8
2.032.0788.610.4261.3342.8
1.982.038810.4861.3352.8
1.951.9887.910.5851.4022.8
1.911.9586.910.6851.4062.8
1.881.9186.210.7991.3772.6
ReflectionResolution: 1.88→50 Å / Num. obs: 227793 / % possible obs: 93.1 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.128 / Net I/σ(I): 7.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.88-1.912.60.799186.2
1.91-1.952.80.685186.9
1.95-1.982.80.585187.9
1.98-2.032.80.486188
2.03-2.072.80.426188.6
2.07-2.122.80.356189.6
2.12-2.172.80.316190.4
2.17-2.232.80.28191.1
2.23-2.292.80.256191.8
2.29-2.372.80.23192.4
2.37-2.452.80.206193.6
2.45-2.552.80.179194.7
2.55-2.672.80.156195.1
2.67-2.812.80.133196
2.81-2.982.80.115196.6
2.98-3.212.80.096197.4
3.21-3.542.80.08198.1
3.54-4.052.80.067199
4.05-5.12.70.055199.1
5.1-502.90.052199.3

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.88→8 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.906 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 7.645 / SU ML: 0.104 / SU R Cruickshank DPI: 0.182 / Cross valid method: THROUGHOUT / ESU R: 0.182 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24207 5793 5.1 %RANDOM
Rwork0.18539 ---
obs0.18822 108877 93.12 %-
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 mean: 19.857 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å20 Å2
2--0.01 Å2-0 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 1.88→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12134 0 8 1409 13551
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02112546
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2131.93817029
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.55751564
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.06623.495638
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.276152045
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7415101
X-RAY DIFFRACTIONr_chiral_restr0.0840.21792
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0219793
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8623.57608
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.9445012136
X-RAY DIFFRACTIONr_scbond_it6.287504938
X-RAY DIFFRACTIONr_scangle_it0.9714.54878
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.88→1.926 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 356 -
Rwork0.225 6758 -
obs--82.53 %
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)
10.36550.18350.03710.52270.030.37160.0228-0.02770.00360.0672-0.01960.02570.0337-0.0191-0.00320.0210.00110.02470.05050.00150.050617.6132-31.062822.6614
20.52130.27360.15050.69090.11540.5166-0.0069-0.10270.0077-0.0313-0.01280.04370.0082-0.02070.01970.01350.0204-0.00150.06080.00130.004815.17261.827760.5665
30.3792-0.16410.11230.5386-0.07010.26360.0050.04340.00130.0311-0.0125-0.01490.0070.01170.00740.0066-0.00620.01150.041-0.0050.0525-20.49010.91714.5351
40.6472-0.11910.0370.6288-0.03670.5535-0.0304-0.0191-0.0804-0.12270.0262-0.060.00320.14020.00420.0366-0.00340.03080.1404-0.02340.0413-23.1492-29.378453.7682
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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