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- PDB-3ik4: CRYSTAL STRUCTURE OF mandelate racemase/muconate lactonizing prot... -

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Basic information

Entry
Database: PDB / ID: 3ik4
TitleCRYSTAL STRUCTURE OF mandelate racemase/muconate lactonizing protein from Herpetosiphon aurantiacus
ComponentsMandelate racemase/muconate lactonizing protein
KeywordsISOMERASE / STRUCTURAL GENOMICS / ENOLASE / EPIMERASE / PSI-2 / PROTEIN STRUCTURE INITIATIVE / NEW YORK SGX RESEARCH CENTER FOR STRUCTURAL GENOMICS / NYSGXRC
Function / homology
Function and homology information


racemase and epimerase activity / racemase and epimerase activity, acting on amino acids and derivatives / Isomerases; Racemases and epimerases; Acting on amino acids and derivatives / peptide metabolic process / magnesium ion binding
Similarity search - Function
Dipeptide epimerase / 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 ...Dipeptide epimerase / 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
: / Aromatic dipeptide epimerase
Similarity search - Component
Biological speciesHerpetosiphon aurantiacus ATCC 23779 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 2.1 Å
AuthorsPatskovsky, Y. / Toro, R. / Dickey, M. / Iizuka, M. / Sauder, J.M. / Gerlt, J.A. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Homology models guide discovery of diverse enzyme specificities among dipeptide epimerases in the enolase superfamily.
Authors: Lukk, T. / Sakai, A. / Kalyanaraman, C. / Brown, S.D. / Imker, H.J. / Song, L. / Fedorov, A.A. / Fedorov, E.V. / Toro, R. / Hillerich, B. / Seidel, R. / Patskovsky, Y. / Vetting, M.W. / ...Authors: Lukk, T. / Sakai, A. / Kalyanaraman, C. / Brown, S.D. / Imker, H.J. / Song, L. / Fedorov, A.A. / Fedorov, E.V. / Toro, R. / Hillerich, B. / Seidel, R. / Patskovsky, Y. / Vetting, M.W. / Nair, S.K. / Babbitt, P.C. / Almo, S.C. / Gerlt, J.A. / Jacobson, M.P.
History
DepositionAug 5, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Mar 21, 2012Group: Database references
Revision 1.3May 23, 2012Group: Database references
Revision 1.4Nov 21, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.5Feb 10, 2021Group: Derived calculations / Structure summary
Category: audit_author / pdbx_struct_conn_angle ...audit_author / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _pdbx_struct_conn_angle.ptnr1_auth_asym_id ..._audit_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.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 1.6Sep 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

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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)152,19410
Polymers151,8544
Non-polymers3416
Water4,270237
1
A: Mandelate racemase/muconate lactonizing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0032
Polymers37,9631
Non-polymers391
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mandelate racemase/muconate lactonizing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0953
Polymers37,9631
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Mandelate racemase/muconate lactonizing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0953
Polymers37,9631
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Mandelate racemase/muconate lactonizing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0032
Polymers37,9631
Non-polymers391
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Mandelate racemase/muconate lactonizing protein
B: Mandelate racemase/muconate lactonizing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,0975
Polymers75,9272
Non-polymers1703
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3340 Å2
ΔGint-13 kcal/mol
Surface area24950 Å2
MethodPISA
6
C: Mandelate racemase/muconate lactonizing protein
hetero molecules

D: Mandelate racemase/muconate lactonizing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,0975
Polymers75,9272
Non-polymers1703
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y+1/2,-z+11
Buried area3310 Å2
ΔGint-12 kcal/mol
Surface area25010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.026, 93.344, 85.914
Angle α, β, γ (deg.)90.00, 112.60, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Mandelate racemase/muconate lactonizing protein


Mass: 37963.426 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Herpetosiphon aurantiacus ATCC 23779 (bacteria)
Gene: Haur_1114 / Production host: Escherichia coli (E. coli) / References: UniProt: A9B055
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / 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: 2.06 Å3/Da / Density % sol: 40.26 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 7.5
Details: 150MM POTASSIUM BROMIDE, PH 7.5, 30% PEG2000 MME, 10% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.081
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 23, 2009 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.081 Å / Relative weight: 1
ReflectionResolution: 2.07→50 Å / Num. obs: 75228 / % possible obs: 98.9 % / Observed criterion σ(I): -5 / Redundancy: 4.1 % / Biso Wilson estimate: 43.053 Å2 / Rsym value: 0.063 / Net I/σ(I): 7.9
Reflection shellResolution: 2.07→2.14 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 0.9 / % possible all: 91.2

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Processing

Software
NameVersionClassification
PHASER1.2phasing
REFMAC5.3.0034refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: molecular replacement
Starting model: 1JPM

1jpm


Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.935 / SU B: 20.061 / SU ML: 0.247 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.29 / ESU R Free: 0.229 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27531 2147 3 %RANDOM
Rwork0.21676 ---
obs0.21855 68809 99.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.917 Å2
Baniso -1Baniso -2Baniso -3
1--2.51 Å20 Å2-1.49 Å2
2---1.73 Å20 Å2
3---3.09 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10201 0 16 237 10454
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02210481
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2531.9614232
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.46751427
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.66824.3400
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.049151680
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3691556
X-RAY DIFFRACTIONr_chiral_restr0.0850.21679
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027845
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1460.34819
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2910.57039
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.5759
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1190.3133
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1380.514
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.3642.56979
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it7.058411041
X-RAY DIFFRACTIONr_scbond_it10.31533514
X-RAY DIFFRACTIONr_scangle_it12.8445.53177
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.412 133 -
Rwork0.333 4742 -
obs--93.95 %
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)
12.71530.01380.27193.3723-1.20961.3290.2147-0.0731-0.1544-0.1751-0.1392-0.34180.33790.1514-0.0755-0.15690.06090.0785-0.1784-0.0252-0.35230.49719.0786.141
22.2399-1.03210.21612.5764-0.13681.4160.24520.0756-0.0716-0.52580.02450.48810.1077-0.2132-0.2698-0.1643-0.0304-0.0306-0.17680.0857-0.1469-31.71832.019-4.243
35.2805-0.94130.58212.25980.0092.46490.45881.1238-0.2102-0.6104-0.38510.14950.25780.1096-0.07380.09880.1628-0.06270.1132-0.0253-0.1581-16.48856.11134.592
42.0470.00471.4013.34740.58951.97110.0067-0.33710.4953-0.0367-0.22670.7205-0.0993-0.530.2199-0.0077-0.019-0.01870.1225-0.18570.2543-47.44518.93229.098
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 358
2X-RAY DIFFRACTION2B0 - 357
3X-RAY DIFFRACTION3C0 - 357
4X-RAY DIFFRACTION4D0 - 356

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