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- PDB-2yjg: Structure of the lactate racemase apoprotein from Thermoanaerobac... -

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Basic information

Entry
Database: PDB / ID: 2yjg
TitleStructure of the lactate racemase apoprotein from Thermoanaerobacterium thermosaccharolyticum
ComponentsLACTATE RACEMASE APOPROTEIN
KeywordsISOMERASE / NICKEL-DEPENDENT ENZYME
Function / homology
Function and homology information


lactate racemase / lactate racemase activity / metal ion binding
Similarity search - Function
LarA, C-terminal domain / LarA, N-terminal domain / : / : / Lactate racemase C-terminal domain / LarA-like, N-terminal / LarA-like, C-terminal domain / : / Lactate racemase N-terminal domain / 2-enoyl-CoA Hydratase; Chain A, domain 1 ...LarA, C-terminal domain / LarA, N-terminal domain / : / : / Lactate racemase C-terminal domain / LarA-like, N-terminal / LarA-like, C-terminal domain / : / Lactate racemase N-terminal domain / 2-enoyl-CoA Hydratase; Chain A, domain 1 / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesTHERMOANAEROBACTERIUM THERMOSACCHAROLYTICUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsDeclercq, J.P. / Desguin, B. / Soumillion, P. / Hols, P.
CitationJournal: Nat.Commun. / Year: 2014
Title: Lactate Racemase is a Nickel-Dependent Enzyme Activated by a Widespread Maturation System.
Authors: Desguin, B. / Goffin, P. / Viaene, E. / Kleerebezem, M. / Martin-Diaconescu, V. / Maroney, M.J. / Declercq, J. / Soumillion, P. / Hols, P.
History
DepositionMay 19, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 30, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 30, 2014Group: Database references
Revision 1.2May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.3May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_conn.ptnr2_label_seq_id / _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: LACTATE RACEMASE APOPROTEIN
B: LACTATE RACEMASE APOPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,8539
Polymers96,2862
Non-polymers5677
Water10,575587
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2910 Å2
ΔGint-86.5 kcal/mol
Surface area33480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.410, 223.250, 46.140
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.0412, 0.96076, 0.27431), (0.9365, -0.05856, 0.34574), (0.34824, 0.27114, -0.89734)
Vector: 46.825, -52.166, 20.112)

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Components

#1: Protein LACTATE RACEMASE APOPROTEIN


Mass: 48143.082 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) THERMOANAEROBACTERIUM THERMOSACCHAROLYTICUM (bacteria)
Strain: DSM 571 / References: UniProt: D9TQ02, lactate racemase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 587 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE LAST 10 RESIDUES OF THE GIVEN SEQUENCE REPRESENT THE STREPTAG USED FOR PURIFICATION.

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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: 2.06 Å3/Da / Density % sol: 40.3 %
Description: THE MAD METHOD WAS APPLIED TO A HG DERIVATIVE. THE RESULTING PARTIAL MODEL WAS POSITIONED IN THE NATIVE DATA BY MOLECULAR REPLACEMENT
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.5
Details: HANGING DROP. RESERVOIR: 22%(W/V) PEGMME 5000, 0.2 M AMMONIUM SULFATE, 0.1 M MES PH 6.5, 3%(V/V) ETHYLENE GLYCOL. DROP: 1 MICROL PROTEIN AND 1 MICROL RESERVOIR.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979733
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 16, 2011
Details: TWO MIRRORS ARE USED FOR VERTICAL FOCUSSING. THEY ALSO ALLOW TO REJECT HIGH ORDER HARMONICS FOUND IN THE WHITE BEAM.
RadiationMonochromator: FIRST CRYSTAL FLAT AND N2 COOLED. SECOND ONE SAGITALLY BENT. SI(111) OR SI(311)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979733 Å / Relative weight: 1
ReflectionResolution: 1.8→45 Å / Num. obs: 73824 / % possible obs: 97 % / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 29.6 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 16
Reflection shellResolution: 1.8→2 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 4.1 / % possible all: 91

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
Auto-Rickshawphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MAD-SOLVED PARTIAL MODEL

Resolution: 1.8→114.96 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.927 / SU B: 2.965 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.138 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. THERE WERE NO RAMACHANDRAN OUTLIERS USING THE MOLPROBITY DEFINITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22933 3721 5 %RANDOM
Rwork0.18169 ---
obs0.18407 70103 97.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.72 Å2
Baniso -1Baniso -2Baniso -3
1--0.53 Å20 Å20 Å2
2--1.22 Å20 Å2
3----0.68 Å2
Refinement stepCycle: LAST / Resolution: 1.8→114.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6459 0 30 587 7076
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0226588
X-RAY DIFFRACTIONr_bond_other_d0.0010.024511
X-RAY DIFFRACTIONr_angle_refined_deg1.7291.9718887
X-RAY DIFFRACTIONr_angle_other_deg0.971311084
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0915831
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.05125.139288
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.775151212
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6461534
X-RAY DIFFRACTIONr_chiral_restr0.1060.21007
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0217259
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021211
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_it1.0531.54143
X-RAY DIFFRACTIONr_mcbond_other0.3181.51696
X-RAY DIFFRACTIONr_mcangle_it1.81726684
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.00732445
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.8394.52203
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.802→1.849 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 232 -
Rwork0.262 4538 -
obs--85.65 %

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