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- PDB-4j3z: Crystal structure of mandelate racemase/muconate lactonizing enzy... -

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Basic information

Entry
Database: PDB / ID: 4j3z
TitleCrystal structure of mandelate racemase/muconate lactonizing enzyme from Jannaschia sp. CCS1
ComponentsMandelate racemase/muconate lactonizing enzyme
KeywordsISOMERASE / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / NYSGRC / PSI-Biology / New York Structural Genomics Research Consortium
Function / homology
Function and homology information


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 ...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
Mandelate racemase/muconate lactonizing enzyme
Similarity search - Component
Biological speciesJannaschia sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsMalashkevich, V.N. / Bhosle, R. / Toro, R. / Hillerich, B. / Gizzi, A. / Garforth, S. / Kar, A. / Chan, M.K. / Lafluer, J. / Patel, H. ...Malashkevich, V.N. / Bhosle, R. / Toro, R. / Hillerich, B. / Gizzi, A. / Garforth, S. / Kar, A. / Chan, M.K. / Lafluer, J. / Patel, H. / Matikainen, B. / Chamala, S. / Lim, S. / Celikgil, A. / Villegas, G. / Evans, B. / Zenchek, W. / Love, J. / Fiser, A. / Khafizov, K. / Seidel, R. / Bonanno, J.B. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: Crystal structure of mandelate racemase/muconate lactonizing enzyme from Jannaschia sp. CCS1
Authors: Malashkevich, V.N. / Bhosle, R. / Toro, R. / Hillerich, B. / Gizzi, A. / Garforth, S. / Kar, A. / Chan, M.K. / Lafluer, J. / Patel, H. / Matikainen, B. / Chamala, S. / Lim, S. / Celikgil, A. ...Authors: Malashkevich, V.N. / Bhosle, R. / Toro, R. / Hillerich, B. / Gizzi, A. / Garforth, S. / Kar, A. / Chan, M.K. / Lafluer, J. / Patel, H. / Matikainen, B. / Chamala, S. / Lim, S. / Celikgil, A. / Villegas, G. / Evans, B. / Zenchek, W. / Love, J. / Fiser, A. / Khafizov, K. / Seidel, R. / Bonanno, J.B. / Almo, S.C.
History
DepositionFeb 6, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2013Provider: repository / Type: Initial release
Revision 1.1May 8, 2013Group: Structure summary
Revision 1.2Sep 20, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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
B: Mandelate racemase/muconate lactonizing enzyme
C: Mandelate racemase/muconate lactonizing enzyme
D: Mandelate racemase/muconate lactonizing enzyme
E: Mandelate racemase/muconate lactonizing enzyme
F: Mandelate racemase/muconate lactonizing enzyme
G: Mandelate racemase/muconate lactonizing enzyme
H: Mandelate racemase/muconate lactonizing enzyme


Theoretical massNumber of molelcules
Total (without water)371,7708
Polymers371,7708
Non-polymers00
Water21,6361201
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area37170 Å2
ΔGint-154 kcal/mol
Surface area83970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.909, 126.626, 126.777
Angle α, β, γ (deg.)90.000, 90.080, 90.000
Int Tables number4
Space group name H-MP1211
Detailsoctameric

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Components

#1: Protein
Mandelate racemase/muconate lactonizing enzyme


Mass: 46471.312 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Jannaschia sp. (bacteria) / Strain: CCS1 / Gene: 3934113, Jann_1665 / Plasmid: BC-PSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CODON+RIL / References: UniProt: Q28RT0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1201 / 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: 2.74 Å3/Da / Density % sol: 55.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 1.0 M Ammonium phosphate, 0.1 M citrate, pH 5.5, 0.2 M NaCl, 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 15, 2011
RadiationProtocol: SAD / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.747
11h,-k,-l20.091
11-H, -L, -K30.083
11-H, L, K40.079
ReflectionResolution: 2.5→50 Å / Num. obs: 140837 / % possible obs: 96.1 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.176 / Χ2: 1.318 / Net I/σ(I): 4.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.5-2.542.40.98471481.245196.9
2.54-2.592.40.87970161.264197.1
2.59-2.642.40.87470391.266196.5
2.64-2.692.40.78571301.253197.1
2.69-2.752.40.60169971.238196.7
2.75-2.822.40.62271281.259197.2
2.82-2.892.50.49270221.233196.9
2.89-2.962.50.45171331.235197
2.96-3.052.50.37870881.236197
3.05-3.152.50.30971271.236197.3
3.15-3.262.50.26170581.238197.1
3.26-3.392.50.20971761.264197.5
3.39-3.552.50.18570941.284197.1
3.55-3.732.40.13666751.417191
3.73-3.972.40.10365171.496189.9
3.97-4.272.50.09669141.447193.6
4.27-4.72.60.07970701.393196.6
4.7-5.382.50.08371491.375197.1
5.38-6.782.60.0971861.31196.8
6.78-502.60.05271701.654196

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 47.24 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å44.88 Å
Translation2.5 Å44.88 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMAC5.7.0029refinement
PDB_EXTRACT3.11data extraction
CBASSdata collection
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3RCY

3rcy


Resolution: 2.5→44.88 Å / Cor.coef. Fo:Fc: 0.838 / Cor.coef. Fo:Fc free: 0.794 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 3.131 / SU ML: 0.042 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.101 / ESU R Free: 0.058 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2451 6920 5 %RANDOM
Rwork0.2112 ---
obs0.213 137531 99.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 89.76 Å2 / Biso mean: 29.8057 Å2 / Biso min: 11.3 Å2
Baniso -1Baniso -2Baniso -3
1--7.73 Å2-0 Å23.5 Å2
2--0.23 Å20 Å2
3---7.5 Å2
Refinement stepCycle: LAST / Resolution: 2.5→44.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23476 0 0 1201 24677
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01924207
X-RAY DIFFRACTIONr_angle_refined_deg1.1851.94933097
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.89553101
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.73322.7551031
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.62153432
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.87515176
X-RAY DIFFRACTIONr_chiral_restr0.0780.23593
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02219018
LS refinement shellResolution: 2.496→2.56 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.156 465 -
Rwork0.118 9022 -
all-9487 -
obs--93.93 %
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)
10.09320.0239-0.00770.0763-0.01490.0070.01390.003-0.00630.0096-0.011-0.00460.0030.0051-0.00290.00960.0046-0.0060.02050.00080.00547.13990.745442.5209
20.0852-0.00310.05330.03950.01420.07220.01720.0017-0.0057-0.0116-0.0036-0.00590.00880.0007-0.01360.00780.0054-0.00030.016-0.00090.003247.161719.75421.8769
30.0767-0.02320.02580.0299-0.04160.06740.0059-0.0095-0.0063-0.00430.00040.00230.0075-0.0072-0.00630.0029-0.006-0.00040.01620.00160.002318.538614.174958.8087
40.10.0118-0.00340.03680.03490.03940.00320.0038-0.0039-0.0042-0.00260.00330.0002-0.0041-0.00060.0069-0.003-0.00560.0188-0.00150.005418.57643.585215.1648
50.12210.0048-0.03650.00530.00740.05450.0166-0.00530.00280.0047-0.0037-0.0051-0.01020.0096-0.01290.0109-0.0078-0.0030.016-0.00110.006847.031241.201761.5594
60.0898-0.03460.01170.0627-0.0080.03010.01690.00560.006-0.0105-0.0133-0.0006-0.00620.0074-0.00360.0063-0.00140.0020.02010.00180.001647.152660.255820.9719
70.11340.0180.02720.0440.03890.05160.0028-0.00740.00440.0071-0.00140.00320.0009-0.0055-0.00140.00370.00350.00180.0173-0.00130.001918.552257.559847.9993
80.08750.0057-0.00540.0202-0.04040.09240.01220.006-0.00080.0041-0.0010.0043-0.0127-0.0112-0.01110.00560.00710.00050.01620.0020.003218.667546.79574.5506
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 389
2X-RAY DIFFRACTION2B2 - 387
3X-RAY DIFFRACTION3C2 - 387
4X-RAY DIFFRACTION4D1 - 393
5X-RAY DIFFRACTION5E1 - 388
6X-RAY DIFFRACTION6F2 - 387
7X-RAY DIFFRACTION7G2 - 387
8X-RAY DIFFRACTION8H1 - 388

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