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- PDB-26tb: Crystal structure of 4-Amino-4-deoxychorismate lyase from Micromo... -

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Entry
Database: PDB / ID: 26tb
TitleCrystal structure of 4-Amino-4-deoxychorismate lyase from Micromonospora aurantiaca ATCC 27029 (holo form) in complex with chorismate
Components4-Amino-4-deoxychorismate lyase
KeywordsLYASE / holoform / 4-Amino-4-deoxychorismate lyase / PLP form / chorismate / complex
Function / homologyChem-ISJ
Function and homology information
Biological speciesMicromonospora aurantiaca ATCC 27029 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsMatyuta, I.O. / Bakunova, A.K. / Bezsudnova, E.Y. / Minyaev, M.E. / Popov, V.O. / Boyko, K.M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of 4-Amino-4-deoxychorismate lyase from Micromonospora aurantiaca ATCC 27029 in holo form and complex with chorismate
Authors: Bakunova, A.K. / Matyuta, I.O. / Minyaev, M.E. / Boyko, K.M. / Popov, V.O. / Bezsudnova, E.Y.
History
DepositionMay 14, 2026Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 27, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 4-Amino-4-deoxychorismate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3834
Polymers29,8271
Non-polymers5573
Water4,342241
1
A: 4-Amino-4-deoxychorismate lyase
hetero molecules

A: 4-Amino-4-deoxychorismate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7678
Polymers59,6542
Non-polymers1,1136
Water362
TypeNameSymmetry operationNumber
point symmetry operation1
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.741, 88.900, 70.333
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein 4-Amino-4-deoxychorismate lyase


Mass: 29826.865 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Micromonospora aurantiaca ATCC 27029 (bacteria)
Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ISJ / (3R,4R)-3-[(1-carboxyethenyl)oxy]-4-hydroxycyclohexa-1,5-diene-1-carboxylic acid / Chorismic Acid


Mass: 226.183 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H10O6 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.22 Å3/Da / Density % sol: 44.61 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100 mM HEPES buffer, pH 7.0, 10 mM MgCl2, 5 mM NiCl2, 20% (v/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54184 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Jan 27, 2026
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 1.85→21.89 Å / Num. obs: 22873 / % possible obs: 99.4 % / Redundancy: 10.2 % / CC1/2: 0.995 / Rmerge(I) obs: 0.182 / Rpim(I) all: 0.059 / Rrim(I) all: 0.191 / Χ2: 0.99 / Net I/σ(I): 12.7 / Num. measured all: 232318
Reflection shellResolution: 1.85→1.89 Å / % possible obs: 96.4 % / Redundancy: 7.8 % / Rmerge(I) obs: 0.799 / Num. measured all: 10401 / Num. unique obs: 1335 / CC1/2: 0.759 / Rpim(I) all: 0.299 / Rrim(I) all: 0.857 / Χ2: 0.94 / Net I/σ(I) obs: 2.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
CrysalisProdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→21.89 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.921 / SU B: 2.965 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.136 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21037 1136 5 %RANDOM
Rwork0.16477 ---
obs0.16697 21723 99.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.892 Å2
Baniso -1Baniso -2Baniso -3
1--0.4 Å2-0 Å20 Å2
2---0.18 Å2-0 Å2
3---0.57 Å2
Refinement stepCycle: 1 / Resolution: 1.85→21.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2078 0 37 241 2356
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0132173
X-RAY DIFFRACTIONr_bond_other_d0.0030.0142076
X-RAY DIFFRACTIONr_angle_refined_deg1.7311.6532988
X-RAY DIFFRACTIONr_angle_other_deg1.3911.5674780
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9575281
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.32418.38499
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.33715297
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6961523
X-RAY DIFFRACTIONr_chiral_restr0.0940.2278
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022434
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02459
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_it1.0371.2211125
X-RAY DIFFRACTIONr_mcbond_other1.0361.2171124
X-RAY DIFFRACTIONr_mcangle_it1.6181.8231404
X-RAY DIFFRACTIONr_mcangle_other1.6171.8271405
X-RAY DIFFRACTIONr_scbond_it1.6881.4181048
X-RAY DIFFRACTIONr_scbond_other1.6881.4191049
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.5812.0691584
X-RAY DIFFRACTIONr_long_range_B_refined4.09215.7032376
X-RAY DIFFRACTIONr_long_range_B_other3.80315.1892313
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 76 -
Rwork0.228 1528 -
obs--96.28 %

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