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- PDB-4lut: alanine racemase [Clostridium difficile 630] complex with cycloserine -

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Basic information

Entry
Database: PDB / ID: 4lut
Titlealanine racemase [Clostridium difficile 630] complex with cycloserine
Components(Alanine racemase) x 2
KeywordsISOMERASE/ISOMERASE INHIBITOR / ISOMERASE-ISOMERASE INHIBITOR complex
Function / homology
Function and homology information


alanine racemase / D-alanine biosynthetic process / alanine racemase activity / peptidoglycan biosynthetic process / pyridoxal phosphate binding / 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-DCS / Alanine racemase
Similarity search - Component
Biological speciesClostridium difficile (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsAsojo, O.A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structural and biochemical analyses of alanine racemase from the multidrug-resistant Clostridium difficile strain 630.
Authors: Asojo, O.A. / Nelson, S.K. / Mootien, S. / Lee, Y. / Rezende, W.C. / Hyman, D.A. / Matsumoto, M.M. / Reiling, S. / Kelleher, A. / Ledizet, M. / Koski, R.A. / Anthony, K.G.
History
DepositionJul 25, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 4, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 23, 2014Group: Database references
Revision 1.2Sep 20, 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 / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alanine racemase
B: Alanine racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,4394
Polymers86,7732
Non-polymers6662
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7070 Å2
ΔGint-22 kcal/mol
Surface area28170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.840, 138.970, 144.890
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 3 - 384 / Label seq-ID: 3 - 384

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Alanine racemase


Mass: 43364.949 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium difficile (bacteria) / Strain: 630 / Gene: alr2, CD630_34630 / Production host: Pichia pastoris (fungus) / References: UniProt: Q180W0, alanine racemase
#2: Protein Alanine racemase


Mass: 43407.949 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Carboxylic modified Lysine / Source: (gene. exp.) Clostridium difficile (bacteria) / Strain: 630 / Gene: alr2, CD630_34630 / Production host: Pichia pastoris (fungus) / References: UniProt: Q180W0, alanine racemase
#3: Chemical ChemComp-DCS / D-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-N,O-CYCLOSERYLAMIDE / D-PYRIDOXYL-N,O-CYCLOSERYLAMIDE-5-MONOPHOSPHATE


Mass: 333.234 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H16N3O7P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 3.36 Å3/Da / Density % sol: 63.42 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20mg/ml protein in 50mM Tris pH 8.0, 0.02% v/v BME, 10 micromolar pyridoxal-L-phosphate, crystallization buffer 0.1M cycloserine, 0.2M sodium formate, 20% w/V PEG3350, VAPOR DIFFUSION, ...Details: 20mg/ml protein in 50mM Tris pH 8.0, 0.02% v/v BME, 10 micromolar pyridoxal-L-phosphate, crystallization buffer 0.1M cycloserine, 0.2M sodium formate, 20% w/V PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.514179 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Oct 5, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.514179 Å / Relative weight: 1
ReflectionResolution: 2.26→53.72 Å / Num. all: 30908 / Num. obs: 35794 / % possible obs: 64.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.7 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 8.7
Reflection shellResolution: 2.26→2.33 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.893 / Mean I/σ(I) obs: 1.8 / Num. unique all: 2605 / % possible all: 55.5

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.7.0032refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4LUS

4lus


Resolution: 2.26→45.62 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.915 / SU B: 14.208 / SU ML: 0.168 / Cross valid method: THROUGHOUT / ESU R: 0.468 / ESU R Free: 0.284 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24788 1785 5 %RANDOM
Rwork0.21014 ---
obs0.21198 33808 63.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.349 Å2
Baniso -1Baniso -2Baniso -3
1--1.64 Å20 Å2-0 Å2
2--1.24 Å2-0 Å2
3---0.41 Å2
Refinement stepCycle: LAST / Resolution: 2.26→45.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5846 0 44 171 6061
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0196118
X-RAY DIFFRACTIONr_bond_other_d0.0030.026038
X-RAY DIFFRACTIONr_angle_refined_deg1.3521.9878257
X-RAY DIFFRACTIONr_angle_other_deg0.977313926
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8895756
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.63125.424271
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.348151159
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4051529
X-RAY DIFFRACTIONr_chiral_restr0.0710.2952
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026814
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021269
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_it1.5751.8093039
X-RAY DIFFRACTIONr_mcbond_other1.5711.8093039
X-RAY DIFFRACTIONr_mcangle_it2.4732.7073790
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.2272.0543079
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined6.40421.4449556
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 23598 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.26→2.319 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 123 -
Rwork0.302 2104 -
obs--54.48 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8075-0.2922-0.16181.2733-0.1951.25830.013-0.08630.08220.05330.00630.0922-0.16980.0139-0.01930.0484-0.00610.00130.0115-0.01950.114825.34139.39492.528
21.19530.0446-0.05491.2949-0.16931.0684-0.0132-0.095-0.01460.10260.0059-0.1030.06050.10510.00730.06080.01250.01140.02150.02060.117845.69222.10893.362
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 384
2X-RAY DIFFRACTION2B3 - 384

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