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- PDB-3s5s: Crystal structure of putative mandelate racemase/muconate lactoni... -

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Basic information

Entry
Database: PDB / ID: 3s5s
TitleCrystal structure of putative mandelate racemase/muconate lactonizing enzyme (PSI/COM target 200551) from Sorangium cellulosum
ComponentsMandelate racemase/muconate lactonizing enzyme family protein
KeywordsISOMERASE / PSI-Biology / Structural Genomics / New York Structural Genomics Research Consortium / NYSGRC
Function / homology
Function and homology information


racemase and epimerase activity, acting on amino acids and derivatives / Isomerases; Racemases and epimerases; Acting on amino acids and derivatives / metal 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
Biological speciesSorangium cellulosum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsRamagopal, U.A. / Toro, R. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be published
Title: Crystal structure of putative mandelate racemase/muconate lactonizing enzyme (PSI/COM target 200551) from Sorangium cellulosum
Authors: Ramagopal, U.A. / Toro, R. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC)
History
DepositionMay 23, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 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 / 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 / _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 family protein
B: Mandelate racemase/muconate lactonizing enzyme family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,4816
Polymers80,0972
Non-polymers3844
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint-66 kcal/mol
Surface area26210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.365, 96.365, 152.354
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Mandelate racemase/muconate lactonizing enzyme family protein


Mass: 40048.293 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sorangium cellulosum (bacteria) / Strain: So ce56 / Gene: sce2857 / Plasmid: CSH30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL / References: UniProt: A9GEI3
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 2.21 Å3/Da / Density % sol: 44.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 0.5M Ammonium Sulfate, 1.0 M Lithium sulfate monohydrate, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 19, 2010
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 28882 / % possible obs: 99.9 % / Redundancy: 10.5 % / Rmerge(I) obs: 0.162 / Χ2: 0.956 / Net I/σ(I): 5.2
Reflection shell
Resolution (Å)Redundancy (%)Num. unique allΧ2Diffraction-ID% possible allRmerge(I) obs
2.4-2.4410.714140.9721100
2.44-2.4910.714190.97711000.919
2.49-2.5310.814170.95911000.879
2.53-2.5910.714040.98711000.778
2.59-2.6410.714010.97811000.692
2.64-2.710.714260.97211000.645
2.7-2.7710.714290.99611000.537
2.77-2.8510.714270.98411000.458
2.85-2.9310.714210.96211000.375
2.93-3.0210.714240.96811000.325
3.02-3.1310.614220.97311000.275
3.13-3.2610.614400.93911000.213
3.26-3.4110.614460.93611000.178
3.41-3.5810.614470.9511000.135
3.58-3.8110.514391.076199.90.11
3.81-4.110.514541.10611000.091
4.1-4.5210.314621.173199.90.081
4.52-5.1710.114740.781199.70.062
5.17-6.519.915110.783199.60.064
6.51-509.716050.65198.80.033

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IK4

3ik4


Resolution: 2.4→48.18 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.884 / WRfactor Rfree: 0.2264 / WRfactor Rwork: 0.1674 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8295 / SU B: 18.259 / SU ML: 0.196 / SU R Cruickshank DPI: 0.5109 / SU Rfree: 0.2946 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.295 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2625 1386 5 %RANDOM
Rwork0.1928 ---
obs0.1962 27520 95.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 86.2 Å2 / Biso mean: 32.7507 Å2 / Biso min: 7.65 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å20 Å2
2---0.08 Å20 Å2
3---0.16 Å2
Refinement stepCycle: LAST / Resolution: 2.4→48.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5158 0 20 66 5244
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0225376
X-RAY DIFFRACTIONr_angle_refined_deg1.721.9737308
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2585745
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.54422.381210
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.86115819
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8011560
X-RAY DIFFRACTIONr_chiral_restr0.1070.2841
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214131
X-RAY DIFFRACTIONr_mcbond_it0.811.53630
X-RAY DIFFRACTIONr_mcangle_it1.48525708
X-RAY DIFFRACTIONr_scbond_it2.74731746
X-RAY DIFFRACTIONr_scangle_it4.394.51600
LS refinement shellResolution: 2.398→2.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 69 -
Rwork0.202 1232 -
all-1301 -
obs--62.64 %
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)
11.59470.465-0.1171.25580.11411.96650.00990.178-0.2764-0.04540.0465-0.23730.11580.2987-0.05630.05870.0288-0.02350.0993-0.03290.08619.05815.55748.521
21.51820.33670.04410.88320.1840.73410.02060.04210.1842-0.024-0.00430.0479-0.2035-0.0295-0.01630.09120.00280.00850.06160.00940.0181-1.30550.05456.208
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 373
2X-RAY DIFFRACTION1A392 - 419
3X-RAY DIFFRACTION2B3 - 360
4X-RAY DIFFRACTION2B392 - 429

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