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- PDB-3ozm: Crystal structure of enolase superfamily member from Bordetella b... -

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Basic information

Entry
Database: PDB / ID: 3ozm
TitleCrystal structure of enolase superfamily member from Bordetella bronchiseptica complexed with Mg, m-Xylarate and L-Lyxarate
ComponentsPutative mandelate racemase
KeywordsTRANSFERASE / alpha-beta Barrel / enolase superfamily member / function unknown / slow substrate m-Xylarate / m-Xylarate Binding
Function / homology
Function and homology information


amino acid catabolic process / hydro-lyase activity / metal ion binding
Similarity search - Function
: / 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 ...: / 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
D-xylaric acid / L-arabinaric acid / Mandelate racemase / Putative mandelate racemase
Similarity search - Component
Biological speciesBordetella bronchiseptica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsFedorov, A.A. / Fedorov, E.V. / Wichelecki, D. / Gerlt, J.A. / Almo, S.C.
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of enolase superfamily member from Bordetella bronchiseptica complexed with Mg, m-Xylarate and L-Lyxarate
Authors: Fedorov, A.A. / Fedorov, E.V. / Wichelecki, D. / Gerlt, J.A. / Almo, S.C.
History
DepositionSep 25, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _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_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_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: Putative mandelate racemase
B: Putative mandelate racemase
C: Putative mandelate racemase
D: Putative mandelate racemase
E: Putative mandelate racemase
F: Putative mandelate racemase
G: Putative mandelate racemase
H: Putative mandelate racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)342,12534
Polymers339,5698
Non-polymers2,55626
Water41,8312322
1
A: Putative mandelate racemase
F: Putative mandelate racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,3937
Polymers84,8922
Non-polymers5015
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2860 Å2
ΔGint-9 kcal/mol
Surface area27760 Å2
MethodPISA
2
B: Putative mandelate racemase
E: Putative mandelate racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,5779
Polymers84,8922
Non-polymers6857
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint-10 kcal/mol
Surface area27700 Å2
MethodPISA
3
C: Putative mandelate racemase
G: Putative mandelate racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,66910
Polymers84,8922
Non-polymers7778
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint-9 kcal/mol
Surface area27780 Å2
MethodPISA
4
D: Putative mandelate racemase
H: Putative mandelate racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,4858
Polymers84,8922
Non-polymers5936
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3200 Å2
ΔGint-8 kcal/mol
Surface area27840 Å2
MethodPISA
5


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area35480 Å2
ΔGint-41 kcal/mol
Surface area88270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.175, 134.335, 146.754
Angle α, β, γ (deg.)90.00, 97.03, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
Putative mandelate racemase /


Mass: 42446.082 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella bronchiseptica (bacteria) / Gene: BB4687 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7WEE8, UniProt: A0A0H3LT39*PLUS

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Non-polymers , 5 types, 2348 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-DXL / D-xylaric acid / m-Xylarate


Mass: 180.113 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C5H8O7
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-LY9 / L-arabinaric acid / L-Lyxarate


Mass: 180.113 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H8O7
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2322 / 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: 2.63 Å3/Da / Density % sol: 53.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 10% PEG 5000, 0.1M Hepes, 5% tacsimate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 9, 2010
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.6→38.999 Å / Num. all: 439058 / Num. obs: 439058 / % possible obs: 95.43 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
BALBESphasing
PHENIX(phenix.refine: 1.5_2)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→38.999 Å / SU ML: 0.23 / σ(F): 0 / Phase error: 25.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2217 22026 5.02 %RANDOM
Rwork0.191 ---
all0.1926 439058 --
obs0.1926 439058 95.43 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.073 Å2 / ksol: 0.35 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.8328 Å20 Å25.5961 Å2
2---2.2202 Å2-0 Å2
3----0.6125 Å2
Refinement stepCycle: LAST / Resolution: 1.6→38.999 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23629 0 164 2322 26115
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00624834
X-RAY DIFFRACTIONf_angle_d1.03233850
X-RAY DIFFRACTIONf_dihedral_angle_d16.5299044
X-RAY DIFFRACTIONf_chiral_restr0.0743720
X-RAY DIFFRACTIONf_plane_restr0.0054484
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.61820.36274700.32249157X-RAY DIFFRACTION63
1.6182-1.63720.33695470.322210050X-RAY DIFFRACTION69
1.6372-1.65720.3415860.321510948X-RAY DIFFRACTION75
1.6572-1.67820.33436180.321611893X-RAY DIFFRACTION82
1.6782-1.70020.33316780.316612985X-RAY DIFFRACTION89
1.7002-1.72350.33047390.301213646X-RAY DIFFRACTION94
1.7235-1.74820.30467180.295914262X-RAY DIFFRACTION98
1.7482-1.77430.31987720.287214387X-RAY DIFFRACTION99
1.7743-1.8020.30077410.26714442X-RAY DIFFRACTION100
1.802-1.83150.28337760.257614490X-RAY DIFFRACTION100
1.8315-1.86310.29047360.249314558X-RAY DIFFRACTION100
1.8631-1.8970.27747710.226814491X-RAY DIFFRACTION100
1.897-1.93350.25967960.218614462X-RAY DIFFRACTION100
1.9335-1.97290.24757830.206414421X-RAY DIFFRACTION100
1.9729-2.01580.22987850.197514460X-RAY DIFFRACTION100
2.0158-2.06270.23718130.196414451X-RAY DIFFRACTION100
2.0627-2.11430.23397570.184214541X-RAY DIFFRACTION100
2.1143-2.17150.2257520.182614456X-RAY DIFFRACTION99
2.1715-2.23540.20427520.171214515X-RAY DIFFRACTION100
2.2354-2.30750.22677680.177414501X-RAY DIFFRACTION100
2.3075-2.390.23167570.170814544X-RAY DIFFRACTION100
2.39-2.48560.22097350.176314618X-RAY DIFFRACTION100
2.4856-2.59870.21327700.173814552X-RAY DIFFRACTION100
2.5987-2.73570.22127280.172714580X-RAY DIFFRACTION100
2.7357-2.90710.21377750.174714572X-RAY DIFFRACTION100
2.9071-3.13140.19197840.170514591X-RAY DIFFRACTION100
3.1314-3.44640.19427450.166214604X-RAY DIFFRACTION100
3.4464-3.94470.17348000.151614597X-RAY DIFFRACTION100
3.9447-4.96830.168110.14214606X-RAY DIFFRACTION100
4.9683-39.01040.18137630.169114652X-RAY DIFFRACTION99

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