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- PDB-2ggj: The mutant Y218C of Deinococcus Radiodurans N-acylamino acid racemase -

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Basic information

Entry
Database: PDB / ID: 2ggj
TitleThe mutant Y218C 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 activity / o-succinylbenzoate synthase / 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: 2.5 Å
AuthorsWang, W.C. / Chiu, W.C.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Structure-Stability-Activity Relationship in Covalently Cross-linked N-Carbamoyl d-Amino acid Amidohydrolase and N-Acylamino acid Racemase.
Authors: Chiu, W.C. / You, J.Y. / Liu, J.S. / Hsu, S.K. / Hsu, W.H. / Shih, C.H. / Hwang, J.K. / Wang, W.C.
History
DepositionMar 24, 2006Deposition site: RCSB / Processing site: PDBJ
SupersessionApr 11, 2006ID: 2FKT
Revision 1.0Apr 11, 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

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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)164,0034
Polymers164,0034
Non-polymers00
Water13,709761
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)328,0058
Polymers328,0058
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)328,0058
Polymers328,0058
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)116.514, 116.514, 120.233
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number75
Space group name H-MP4
DetailsThe biological assembly is a octamer.

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Components

#1: Protein
N-acylamino acid racemase


Mass: 41000.633 Da / Num. of mol.: 4 / Mutation: Y218C
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: UniProt: Q9RYA6, amino-acid racemase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 761 / 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: 2.49 Å3/Da / Density % sol: 50.54 %
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: Nov 12, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 55568 / % possible obs: 99.7 %
Reflection shellResolution: 2.5→2.59 Å / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1R0M

1r0m


Resolution: 2.5→30 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.915 / SU B: 6.859 / SU ML: 0.155 / Cross valid method: THROUGHOUT / ESU R: 0.342 / ESU R Free: 0.251 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20806 2806 5.1 %RANDOM
Rwork0.16214 ---
all0.164 ---
obs0.16445 52558 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: 16.743 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20 Å20 Å2
2--0.13 Å20 Å2
3----0.25 Å2
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11040 0 0 761 11801
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02111240
X-RAY DIFFRACTIONr_angle_refined_deg1.4021.96515248
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.11451432
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.12922.835508
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.834151872
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9815124
X-RAY DIFFRACTIONr_chiral_restr0.0880.21728
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028560
X-RAY DIFFRACTIONr_nbd_refined0.2380.35739
X-RAY DIFFRACTIONr_nbtor_refined0.3230.57705
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.230.51382
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1590.382
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.230.541
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 206 -
Rwork0.204 3841 -
obs--99.85 %

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