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- PDB-3n6j: Crystal structure of Mandelate racemase/muconate lactonizing prot... -

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Basic information

Entry
Database: PDB / ID: 3n6j
TitleCrystal structure of Mandelate racemase/muconate lactonizing protein from Actinobacillus succinogenes 130Z
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


amino acid catabolic process / metal ion binding
Similarity search - Function
D-Glucarate dehydratase-like / Mandelate racemase / muconate lactonizing enzyme family signature 1. / Mandelate racemase/muconate lactonizing enzyme, conserved site / 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 ...D-Glucarate dehydratase-like / Mandelate racemase / muconate lactonizing enzyme family signature 1. / Mandelate racemase/muconate lactonizing enzyme, conserved site / 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 protein
Similarity search - Component
Biological speciesActinobacillus succinogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsMalashkevich, V.N. / Toro, R. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York Structural GenomiX Research Consortium (NYSGXRC) / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of Mandelate racemase/muconate lactonizing protein from Actinobacillus succinogenes 130Z
Authors: Malashkevich, V.N. / Toro, R. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionMay 25, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: 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 / Structure summary / Category: audit_author / 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 / struct_conn / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.5Sep 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 1.6Nov 22, 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


Theoretical massNumber of molelcules
Total (without water)205,2604
Polymers205,2604
Non-polymers00
Water6,233346
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10700 Å2
ΔGint-23 kcal/mol
Surface area58850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.781, 84.347, 113.475
Angle α, β, γ (deg.)90.00, 97.92, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Mandelate racemase/muconate lactonizing protein


Mass: 51314.910 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinobacillus succinogenes (bacteria) / Strain: 130Z / Gene: 152979509, Asuc_1852 / Plasmid: BC-PSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CODON+RIL / References: UniProt: A6VQF6
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 346 / 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: 2.1 Å3/Da / Density % sol: 41.33 %
Description: SUBUNITS A AND B ARE WELL ORDERED AND SUBUNITS C AND D ARE HIGHLY DISORDERED.
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25% PEG 1500, pH 7.5, 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 15, 2010
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 54729 / % possible obs: 82.1 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.118 / Net I/σ(I): 7.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obs% possible all
2.4-2.4440.74153.5
2.44-2.494.10.74557.3
2.49-2.534.10.63860.4
2.53-2.594.20.57864.1
2.59-2.644.30.5466.3
2.64-2.74.30.55969.6
2.7-2.774.30.46674.4
2.77-2.854.20.40280.1
2.85-2.934.10.36186.5
2.93-3.024.10.30690.6
3.02-3.1340.24893.2
3.13-3.2640.19694.9
3.26-3.413.90.14595.9
3.41-3.583.80.12196
3.58-3.813.70.09995.1
3.81-4.13.60.07995.5
4.1-4.523.50.07294
4.52-5.173.50.06393
5.17-6.513.40.06291.5
6.51-503.40.04888.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 43.19 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å39.26 Å
Translation2.5 Å39.26 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EC7

1ec7


Resolution: 2.4→19.95 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.81 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 28.294 / SU ML: 0.303 / SU R Cruickshank DPI: 0.344 / Cross valid method: THROUGHOUT / ESU R Free: 0.48 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30389 2309 5.1 %RANDOM
Rwork0.21721 ---
obs0.22161 43205 68.48 %-
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: 34.976 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20.04 Å2
2---0.03 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.4→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13709 0 0 346 14055
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02214081
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2341.94919130
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.79951759
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.8524.432643
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.977152326
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9281572
X-RAY DIFFRACTIONr_chiral_restr0.0820.22075
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02110801
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_it0.6273.58724
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.1465014037
X-RAY DIFFRACTIONr_scbond_it7.458505357
X-RAY DIFFRACTIONr_scangle_it0.6214.55089
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.43 40 -
Rwork0.226 743 -
obs--16.19 %
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)
10.6608-0.1102-0.25331.62750.35041.0111-0.05080.0915-0.1109-0.059-0.02520.3090.0812-0.05340.0760.057-0.0083-0.04120.09710.00380.105425.0427-8.39873.6527
20.98880.0395-0.58491.27860.34351.16850.0030.00590.1530.0999-0.01090.2979-0.1327-0.00520.00790.12480.0256-0.00060.02720.01880.136319.492429.715124.0559
31.42290.20380.85620.46860.16861.44070.0108-0.25030.03860.1131-0.10320.08480.1083-0.10930.09230.2810.04710.140.13470.03040.077321.9731-9.950755.522
40.88560.07070.48271.12220.44121.038-0.0246-0.26180.1253-0.0319-0.20330.25120.0359-0.42470.22790.0512-0.01480.08060.2839-0.10480.2379-15.3245-8.126332.554
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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