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- PDB-2fkp: The mutant G127C-T313C of Deinococcus Radiodurans N-acylamino aci... -

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Basic information

Entry
Database: PDB / ID: 2fkp
TitleThe mutant G127C-T313C of Deinococcus Radiodurans N-acylamino acid racemase
ComponentsN-acylamino acid racemase
KeywordsISOMERASE / N-Acylamino Acid Racemase / Deinococcus Radiodurans
Function / homology
Function and homology information


o-succinylbenzoate synthase / O-succinylbenzoate synthase activity / Isomerases; Racemases and epimerases; Acting on amino acids and derivatives / menaquinone biosynthetic process / isomerase activity / metal ion binding
Similarity search - Function
o-Succinylbenzoate synthase, MenC type 2 / 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 ...o-Succinylbenzoate synthase, MenC type 2 / 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
: / N-succinylamino acid racemase
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWang, W.C. / Chiu, W.C.
CitationJournal: To be Published
Title: Enhanced thermoactivity in covalently cross-linked N-carbamoyl D-amino acid amidohydrolase but not in N-acylamino acid racemase that has induced fit movements upon substrate binding
Authors: Wang, W.C. / Chiu, W.C.
History
DepositionJan 5, 2006Deposition site: RCSB / Processing site: PDBJ
SupersessionJan 24, 2006ID: 2BAH
Revision 1.0Jan 24, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Oct 25, 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

Downloads & links

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Assembly

Deposited unit
A: N-acylamino acid racemase
B: N-acylamino acid racemase
C: N-acylamino acid racemase
D: N-acylamino acid racemase


Theoretical massNumber of molelcules
Total (without water)164,4354
Polymers164,4354
Non-polymers00
Water16,051891
1
A: N-acylamino acid racemase
C: N-acylamino acid racemase

A: N-acylamino acid racemase
C: N-acylamino acid racemase

A: N-acylamino acid racemase
C: N-acylamino acid racemase

A: N-acylamino acid racemase
C: N-acylamino acid racemase


Theoretical massNumber of molelcules
Total (without water)328,8708
Polymers328,8708
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
2
B: N-acylamino acid racemase
D: N-acylamino acid racemase

B: N-acylamino acid racemase
D: N-acylamino acid racemase

B: N-acylamino acid racemase
D: N-acylamino acid racemase

B: N-acylamino acid racemase
D: N-acylamino acid racemase


Theoretical massNumber of molelcules
Total (without water)328,8708
Polymers328,8708
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Unit cell
Length a, b, c (Å)116.129, 116.129, 120.536
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number75
Space group name H-MP4
Components on special symmetry positions
IDModelComponents
11C-464-

HOH

21D-461-

HOH

DetailsThe biological assembly is an octamer.

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Components

#1: Protein
N-acylamino acid racemase


Mass: 41108.797 Da / Num. of mol.: 4 / Mutation: G127C,T313C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Strain: CCRC 12827 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109
References: GenBank: 15805085, UniProt: Q9RYA6*PLUS, amino-acid racemase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 891 / 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: 2.47 Å3/Da / Density % sol: 50.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: lithium sulfate, Tris-HCl, PEG4000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 24, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 107937 / % possible obs: 97.1 %
Reflection shellResolution: 2→2.07 Å / % possible all: 95.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1R0M

1r0m


Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.92 / SU B: 3.753 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.18 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22715 5219 5 %RANDOM
Rwork0.18202 ---
obs0.18427 99316 97.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.159 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å20 Å20 Å2
2--0.32 Å20 Å2
3----0.65 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11068 0 0 891 11959
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02111272
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2991.96515292
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.95251432
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.19122.812512
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.109151876
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0615124
X-RAY DIFFRACTIONr_chiral_restr0.0850.21728
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028592
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.210.35450
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.57718
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.51582
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1660.375
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2040.567
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.11327349
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.683311396
X-RAY DIFFRACTIONr_scbond_it1.28524430
X-RAY DIFFRACTIONr_scangle_it2.01833896
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 363 -
Rwork0.217 7117 -
obs--95.03 %

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