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- PDB-3qld: Structure of Probable Mandelate Racemase (AaLAA1DRAFT_2112) from ... -

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Basic information

Entry
Database: PDB / ID: 3qld
TitleStructure of Probable Mandelate Racemase (AaLAA1DRAFT_2112) from Alicyclobacillus Acidocaldarius
ComponentsMandelate racemase/muconate lactonizing protein
KeywordsISOMERASE / structural genomics / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


o-succinylbenzoate synthase / O-succinylbenzoate synthase activity / menaquinone biosynthetic process / magnesium ion binding
Similarity search - Function
o-Succinylbenzoate synthase, MenC type 2 / 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 ...o-Succinylbenzoate synthase, MenC type 2 / 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
o-succinylbenzoate synthase
Similarity search - Component
Biological speciesAlicyclobacillus acidocaldarius LAA1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 Å
AuthorsRamagopal, U.A. / Toro, R. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be published
Title: Structure of Probable Mandelate Racemase (AaLAA1DRAFT_2112) from Alicyclobacillus Acidocaldarius
Authors: Ramagopal, U.A. / Toro, R. / Burley, S.K. / Almo, S.C.
History
DepositionFeb 2, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 20, 2011Group: Structure summary
Revision 1.3Nov 9, 2011Group: Structure summary
Revision 1.4Jun 3, 2015Group: Refinement description
Revision 1.5Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_ref_seq_dif / struct_site
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 / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,1287
Polymers86,6482
Non-polymers4805
Water4,234235
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4000 Å2
ΔGint-79 kcal/mol
Surface area30140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.698, 82.054, 77.947
Angle α, β, γ (deg.)90.000, 104.600, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Mandelate racemase/muconate lactonizing protein


Mass: 43324.047 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alicyclobacillus acidocaldarius LAA1 (bacteria)
Gene: AaLAA1DRAFT_2112 / Plasmid: BC-pSGX4(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B7DSY7
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 235 / 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: 1.95 Å3/Da / Density % sol: 37.04 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 30% PEG 8K, 0.2M Ammonium Sulfate, pH 7.0, 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: Apr 22, 2010
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 56819 / % possible obs: 100 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.09 / Χ2: 1.736 / Net I/σ(I): 12.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.85-1.887.40.76428341.277199.9
1.88-1.927.40.61628231.3251100
1.92-1.957.50.51928431.3551100
1.95-1.997.50.42627881.3961100
1.99-2.047.50.37128461.4221100
2.04-2.087.50.29628201.5181100
2.08-2.147.50.25328231.5221100
2.14-2.197.50.2128451.5231100
2.19-2.267.60.18828051.611100
2.26-2.337.50.17328411.7081100
2.33-2.417.50.14828441.6811100
2.41-2.517.50.13328541.7921100
2.51-2.637.50.12228321.8581100
2.63-2.767.50.11128321.9841100
2.76-2.947.50.09828331.8451100
2.94-3.167.50.08828631.9121100
3.16-3.487.40.07928381.8441100
3.48-3.997.30.0728631.8011100
3.99-5.027.10.0628721.9971100
5.02-507.20.06729203.351199.6

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.85→40 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.949 / WRfactor Rfree: 0.2428 / WRfactor Rwork: 0.195 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8376 / SU B: 3.368 / SU ML: 0.104 / SU R Cruickshank DPI: 0.1599 / SU Rfree: 0.144 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.16 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2249 2873 5.1 %RANDOM
Rwork0.1831 ---
obs0.1853 56720 99.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 86.9 Å2 / Biso mean: 32.0699 Å2 / Biso min: 13.55 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å20 Å2
2--0.1 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.85→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5859 0 25 235 6119
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0226106
X-RAY DIFFRACTIONr_angle_refined_deg1.9211.9658318
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.225774
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.51422.391276
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.68615993
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2211571
X-RAY DIFFRACTIONr_chiral_restr0.1440.2930
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214685
X-RAY DIFFRACTIONr_mcbond_it1.2761.53826
X-RAY DIFFRACTIONr_mcangle_it2.18526141
X-RAY DIFFRACTIONr_scbond_it3.41432280
X-RAY DIFFRACTIONr_scangle_it5.4674.52177
LS refinement shellResolution: 1.848→1.896 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 194 -
Rwork0.238 3718 -
all-3912 -
obs--92.05 %

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