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- PDB-4beq: Structure of Vibrio cholerae broad spectrum racemase double mutan... -

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Basic information

Entry
Database: PDB / ID: 4beq
TitleStructure of Vibrio cholerae broad spectrum racemase double mutant R173A, N174A
ComponentsALANINE RACEMASE 2
KeywordsISOMERASE
Function / homology
Function and homology information


methionine racemase activity / ornithine racemase activity / arginine racemase activity / lysine racemase activity / amino-acid racemase / serine racemase activity / D-alanine biosynthetic process / alanine racemase activity / pyridoxal phosphate binding / periplasmic space / cytosol
Similarity search - Function
Racemase Bsr/Lyr / Alanine racemase, pyridoxal-phosphate attachment site / Alanine racemase pyridoxal-phosphate attachment site. / Alanine racemase / Alanine racemase, C-terminal / Alanine racemase, C-terminal domain / Alanine racemase, C-terminal domain / Alanine racemase, N-terminal / Alanine racemase, N-terminal domain / Lyase, Ornithine Decarboxylase; Chain A, domain 1 ...Racemase Bsr/Lyr / Alanine racemase, pyridoxal-phosphate attachment site / Alanine racemase pyridoxal-phosphate attachment site. / Alanine racemase / Alanine racemase, C-terminal / Alanine racemase, C-terminal domain / Alanine racemase, C-terminal domain / Alanine racemase, N-terminal / Alanine racemase, N-terminal domain / Lyase, Ornithine Decarboxylase; Chain A, domain 1 / Lyase, Ornithine Decarboxylase; Chain A, domain 1 / Alanine racemase / Alanine racemase/group IV decarboxylase, C-terminal / PLP-binding barrel / TIM Barrel / Alpha-Beta Barrel / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / Broad specificity amino-acid racemase
Similarity search - Component
Biological speciesVIBRIO CHOLERAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsCarrasco-Lopez, C. / Hermoso, J.A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structural Basis for the Broad Specificity of a New Family of Amino-Acid Racemases.
Authors: Espaillat, A. / Carrasco-Lopez, C. / Bernardo-Garcia, N. / Pietrosemoli, N. / Otero, L.H. / Alvarez, L. / De Pedro, M.A. / Pazos, F. / Davis, B.M. / Waldor, M.K. / Hermoso, J.A. / Cava, F.
History
DepositionMar 12, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 15, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2014Group: Database references
Revision 1.2Jul 9, 2014Group: Database references
Revision 2.0Dec 20, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _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_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
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ALANINE RACEMASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0112
Polymers41,7641
Non-polymers2471
Water7,999444
1
A: ALANINE RACEMASE 2
hetero molecules

A: ALANINE RACEMASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,0234
Polymers83,5282
Non-polymers4942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area7630 Å2
ΔGint-22.1 kcal/mol
Surface area27150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.997, 50.990, 76.455
Angle α, β, γ (deg.)90.00, 100.69, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2215-

HOH

21A-2374-

HOH

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Components

#1: Protein ALANINE RACEMASE 2 /


Mass: 41764.230 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) VIBRIO CHOLERAE (bacteria) / Plasmid: PET28B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9KSE5, alanine racemase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 444 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsPYRIDOXAL-5'-PHOSPHATE (PLP): PLP IS COVALENTLY LINKED TO THE LYS74

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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: 2.18 Å3/Da / Density % sol: 43.61 % / Description: NONE
Crystal growpH: 7.5
Details: 0.1 M BIS-TRIS PROPANE PH 7.5, 0.2 M SODIUM BROMIDE, 29% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99987
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 11, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99987 Å / Relative weight: 1
ReflectionResolution: 1.5→44.8 Å / Num. obs: 57665 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 6.7 % / Biso Wilson estimate: 12.88 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.7
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.08 / Mean I/σ(I) obs: 4.2 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4BEU

4beu


Resolution: 1.5→44.856 Å / SU ML: 0.33 / σ(F): 1.35 / Phase error: 16.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1704 4178 7.2 %
Rwork0.1474 --
obs0.1491 57629 98.86 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.647 Å2 / ksol: 0.396 e/Å3
Displacement parametersBiso mean: 17.1 Å2
Baniso -1Baniso -2Baniso -3
1--1.7748 Å20 Å2-2.3031 Å2
2--0.4747 Å20 Å2
3---1.3001 Å2
Refinement stepCycle: LAST / Resolution: 1.5→44.856 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2928 0 15 444 3387
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013033
X-RAY DIFFRACTIONf_angle_d1.2974119
X-RAY DIFFRACTIONf_dihedral_angle_d12.9311121
X-RAY DIFFRACTIONf_chiral_restr0.073474
X-RAY DIFFRACTIONf_plane_restr0.007538
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.5170.28521260.21611713X-RAY DIFFRACTION97
1.517-1.53490.24091440.19961735X-RAY DIFFRACTION97
1.5349-1.55360.20831370.1821785X-RAY DIFFRACTION97
1.5536-1.57330.22011160.18571702X-RAY DIFFRACTION97
1.5733-1.5940.21911260.17031812X-RAY DIFFRACTION98
1.594-1.61580.18331630.16361699X-RAY DIFFRACTION98
1.6158-1.63890.2051200.1621819X-RAY DIFFRACTION99
1.6389-1.66340.21391520.16831742X-RAY DIFFRACTION98
1.6634-1.68940.19391430.15411762X-RAY DIFFRACTION99
1.6894-1.71710.17871330.15211765X-RAY DIFFRACTION99
1.7171-1.74670.18891150.14751858X-RAY DIFFRACTION99
1.7467-1.77840.17671480.13951716X-RAY DIFFRACTION99
1.7784-1.81260.16781400.14211822X-RAY DIFFRACTION99
1.8126-1.84960.16921310.14751785X-RAY DIFFRACTION99
1.8496-1.88990.17891550.14521737X-RAY DIFFRACTION99
1.8899-1.93380.17921470.14051791X-RAY DIFFRACTION99
1.9338-1.98220.18151300.14261772X-RAY DIFFRACTION100
1.9822-2.03580.18741490.14081806X-RAY DIFFRACTION99
2.0358-2.09570.17841300.13931810X-RAY DIFFRACTION99
2.0957-2.16330.16561410.14061754X-RAY DIFFRACTION99
2.1633-2.24060.16921330.13811801X-RAY DIFFRACTION100
2.2406-2.33040.15271500.13611779X-RAY DIFFRACTION99
2.3304-2.43640.16141490.131802X-RAY DIFFRACTION100
2.4364-2.56480.16731450.13261793X-RAY DIFFRACTION100
2.5648-2.72550.14351170.13151829X-RAY DIFFRACTION99
2.7255-2.93590.16541360.14121778X-RAY DIFFRACTION99
2.9359-3.23130.17351840.14611768X-RAY DIFFRACTION99
3.2313-3.69870.17891510.14461807X-RAY DIFFRACTION99
3.6987-4.65920.12321340.1311824X-RAY DIFFRACTION100
4.6592-44.87610.16871330.18371885X-RAY DIFFRACTION99

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