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

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Basic information

Entry
Database: PDB / ID: 3ozy
TitleCrystal structure of enolase superfamily member from Bordetella bronchiseptica complexed with Mg and m-Xylarate
ComponentsPutative mandelate racemase
KeywordsUNKNOWN FUNCTION / beta-alpha barrel / ENOLASE superfamily member / m-Xylarate
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
ACETIC ACID / D-xylaric acid / Mandelate racemase / Putative mandelate racemase
Similarity search - Component
Biological speciesBordetella bronchiseptica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2994 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 and m-Xylarate
Authors: Fedorov, A.A. / Fedorov, E.V. / Wichelecki, D. / Gerlt, J.A. / Almo, S.C.
History
DepositionSep 27, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 6, 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 / 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_auth_seq_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,89817
Polymers84,8922
Non-polymers1,00615
Water17,781987
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5460 Å2
ΔGint-32 kcal/mol
Surface area26340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.769, 116.769, 128.417
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
Components on special symmetry positions
IDModelComponents
11A-843-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Putative mandelate racemase /


Mass: 42446.082 Da / Num. of mol.: 2
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, 1002 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H4O2
#5: Chemical ChemComp-DXL / D-xylaric acid / m-Xylarate


Mass: 180.113 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H8O7
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 987 / 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: 2.58 Å3/Da / Density % sol: 52.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.8M Sodium Acetate trihydrate, 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: Aug 19, 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: 1.299→37.25 Å / Num. all: 208552 / Num. obs: 208552 / % possible obs: 99.06 % / 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
Starting model: PDB ENTRY 3OZM

3ozm


Resolution: 1.2994→37.25 Å / SU ML: 0.16 / σ(F): 0 / Phase error: 15.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1716 10492 5.03 %RANDOM
Rwork0.1544 ---
all0.1552 208552 --
obs0.1552 208552 99.06 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.957 Å2 / ksol: 0.383 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.9507 Å20 Å2-0 Å2
2--0.9507 Å2-0 Å2
3----1.9014 Å2
Refinement stepCycle: LAST / Resolution: 1.2994→37.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5924 0 64 987 6975
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066302
X-RAY DIFFRACTIONf_angle_d1.1038588
X-RAY DIFFRACTIONf_dihedral_angle_d16.5792285
X-RAY DIFFRACTIONf_chiral_restr0.076938
X-RAY DIFFRACTIONf_plane_restr0.0061144
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2994-1.31420.24332940.25325514X-RAY DIFFRACTION83
1.3142-1.32970.26913220.24826207X-RAY DIFFRACTION93
1.3297-1.34590.2463490.23936461X-RAY DIFFRACTION97
1.3459-1.36290.22673470.22026567X-RAY DIFFRACTION99
1.3629-1.38090.23113450.21026678X-RAY DIFFRACTION100
1.3809-1.39980.20613810.20256585X-RAY DIFFRACTION100
1.3998-1.41980.24713570.19336684X-RAY DIFFRACTION100
1.4198-1.4410.20093520.18276651X-RAY DIFFRACTION100
1.441-1.46350.18453220.17546661X-RAY DIFFRACTION100
1.4635-1.48750.18883590.17256638X-RAY DIFFRACTION100
1.4875-1.51310.18213460.16866724X-RAY DIFFRACTION100
1.5131-1.54060.20323590.1686646X-RAY DIFFRACTION100
1.5406-1.57030.17283650.15646576X-RAY DIFFRACTION100
1.5703-1.60230.18953810.1556672X-RAY DIFFRACTION100
1.6023-1.63720.17323590.14726626X-RAY DIFFRACTION100
1.6372-1.67520.14383760.14386603X-RAY DIFFRACTION100
1.6752-1.71710.15633710.13826692X-RAY DIFFRACTION100
1.7171-1.76360.15963790.13466622X-RAY DIFFRACTION100
1.7636-1.81550.15263140.13636644X-RAY DIFFRACTION100
1.8155-1.87410.15753540.13236682X-RAY DIFFRACTION100
1.8741-1.9410.17353450.13486684X-RAY DIFFRACTION100
1.941-2.01870.14513380.13416687X-RAY DIFFRACTION100
2.0187-2.11060.14543730.13246605X-RAY DIFFRACTION100
2.1106-2.22190.15493480.13166745X-RAY DIFFRACTION100
2.2219-2.36110.15083620.13566613X-RAY DIFFRACTION100
2.3611-2.54330.15913630.14166686X-RAY DIFFRACTION100
2.5433-2.79920.15963420.14496683X-RAY DIFFRACTION100
2.7992-3.20410.1663120.14416711X-RAY DIFFRACTION100
3.2041-4.0360.13183310.12386750X-RAY DIFFRACTION100
4.036-37.26490.15823460.14266763X-RAY DIFFRACTION100

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