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- PDB-4xbj: Y274F alanine racemase from E. coli inhibited by l-ala-p -

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Basic information

Entry
Database: PDB / ID: 4xbj
TitleY274F alanine racemase from E. coli inhibited by l-ala-p
ComponentsAlanine racemase, biosynthetic
KeywordsISOMERASE/ISOMERASE INHIBITOR / ISOMERASE / ISOMERASE-ISOMERASE INHIBITOR complex
Function / homology
Function and homology information


alanine racemase / D-alanine biosynthetic process / alanine racemase activity / peptidoglycan biosynthetic process / cell wall organization / pyridoxal phosphate binding / regulation of cell shape / protein homodimerization activity / cytosol
Similarity search - Function
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 / Lyase, Ornithine Decarboxylase; Chain A, domain 1 / Alanine racemase, N-terminal / Alanine racemase, N-terminal domain / Lyase, Ornithine Decarboxylase; Chain A, domain 1 ...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 / Lyase, Ornithine Decarboxylase; Chain A, domain 1 / Alanine racemase, N-terminal / Alanine racemase, N-terminal domain / 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
Chem-IN5 / Alanine racemase, biosynthetic
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsSquire, C.J. / Yosaatmadja, Y. / Patrick, W.M.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Mechanistic and Evolutionary Insights from the Reciprocal Promiscuity of Two Pyridoxal Phosphate-dependent Enzymes.
Authors: Soo, V.W. / Yosaatmadja, Y. / Squire, C.J. / Patrick, W.M.
History
DepositionDec 17, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 22, 2021Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_struct_oper_list
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alanine racemase, biosynthetic
B: Alanine racemase, biosynthetic
C: Alanine racemase, biosynthetic
D: Alanine racemase, biosynthetic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,58115
Polymers156,7444
Non-polymers1,83711
Water4,252236
1
A: Alanine racemase, biosynthetic
B: Alanine racemase, biosynthetic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,4688
Polymers78,3722
Non-polymers1,0976
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5420 Å2
ΔGint-4 kcal/mol
Surface area26670 Å2
MethodPISA
2
C: Alanine racemase, biosynthetic
D: Alanine racemase, biosynthetic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,1127
Polymers78,3722
Non-polymers7405
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5220 Å2
ΔGint-13 kcal/mol
Surface area26340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.978, 147.978, 163.578
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6

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Components

#1: Protein
Alanine racemase, biosynthetic


Mass: 39185.879 Da / Num. of mol.: 4 / Mutation: Y274F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: alr / Production host: Escherichia coli (E. coli) / References: UniProt: P0A6B4, alanine racemase
#2: Chemical ChemComp-IN5 / {1-[(3-HYDROXY-METHYL-5-PHOSPHONOOXY-METHYL-PYRIDIN-4-YLMETHYL)-AMINO]-ETHYL}-PHOSPHONIC ACID


Mass: 356.206 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H18N2O8P2
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / 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: 3.3 Å3/Da / Density % sol: 62.71 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1 M HEPES pH 7.0, 1.6 M ammonium sulfate

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 28, 2014
RadiationMonochromator: osmic mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.487
11K, H, -L20.513
ReflectionResolution: 2.25→19.91 Å / Num. obs: 95615 / % possible obs: 99.7 % / Redundancy: 11.4 % / CC1/2: 0.992 / Rpim(I) all: 0.088 / Net I/σ(I): 10.7
Reflection shellResolution: 2.25→2.29 Å / Redundancy: 10.2 % / Mean I/σ(I) obs: 2 / CC1/2: 0.617 / Rpim(I) all: 0.432 / % possible all: 97

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WR3

4wr3


Resolution: 2.25→19.9 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.919 / SU B: 2.051 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.04 / ESU R Free: 0.034 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20217 4924 5.1 %RANDOM
Rwork0.16731 ---
obs0.16914 90731 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.717 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å2-0 Å2-0 Å2
2---0.27 Å2-0 Å2
3---0.55 Å2
Refinement stepCycle: LAST / Resolution: 2.25→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10758 0 106 236 11100
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01911165
X-RAY DIFFRACTIONr_bond_other_d00.0210736
X-RAY DIFFRACTIONr_angle_refined_deg1.1421.96315189
X-RAY DIFFRACTIONr_angle_other_deg0.645324586
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.39451424
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.10422.723470
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.011151773
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.29315105
X-RAY DIFFRACTIONr_chiral_restr0.0740.21713
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02112643
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022535
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_it1.8942.1245699
X-RAY DIFFRACTIONr_mcbond_other1.8942.1245698
X-RAY DIFFRACTIONr_mcangle_it2.5053.1747116
X-RAY DIFFRACTIONr_mcangle_other2.5043.1757117
X-RAY DIFFRACTIONr_scbond_it2.0892.2665466
X-RAY DIFFRACTIONr_scbond_other2.0712.2585432
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.8033.3248023
X-RAY DIFFRACTIONr_long_range_B_refined3.8716.74912408
X-RAY DIFFRACTIONr_long_range_B_other3.84316.77112353
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.251→2.31 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.174 328 -
Rwork0.119 6619 -
obs--98.36 %

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