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

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Basic information

Entry
Database: PDB / ID: 26tc
TitleCrystal structure of 4-Amino-4-deoxychorismate lyase from Micromonospora aurantiaca ATCC 27029 in its holo form
Components4-Amino-4-deoxychorismate lyase
KeywordsLYASE / holoform / 4-Amino-4-deoxychorismate lyase / PLP form
Biological speciesMicromonospora aurantiaca ATCC 27029 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)30,3033
Polymers29,8271
Non-polymers4772
Water3,873215
1
A: 4-Amino-4-deoxychorismate lyase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)60,6076
Polymers59,6542
Non-polymers9534
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1
Unit cell
Length a, b, c (Å)84.936, 88.524, 70.182
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.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 2.21 Å3/Da / Density % sol: 44.38 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop
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: Feb 25, 2026
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 2→20.68 Å / Num. obs: 18157 / % possible obs: 99.6 % / Redundancy: 7 % / CC1/2: 0.94 / Rmerge(I) obs: 0.464 / Rpim(I) all: 0.192 / Rrim(I) all: 0.504 / Χ2: 1.04 / Net I/σ(I): 3.7 / Num. measured all: 126637
Reflection shellResolution: 2→2.05 Å / % possible obs: 96.1 % / Redundancy: 7.2 % / Rmerge(I) obs: 1.186 / Num. measured all: 9226 / Num. unique obs: 1287 / CC1/2: 0.557 / Rpim(I) all: 0.483 / Rrim(I) all: 1.284 / Χ2: 0.88 / Net I/σ(I) obs: 1.8

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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: 2→20.68 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.881 / SU B: 6.772 / SU ML: 0.177 / Cross valid method: THROUGHOUT / ESU R: 0.233 / ESU R Free: 0.208 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27985 847 4.7 %RANDOM
Rwork0.21472 ---
obs0.21778 17206 99.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.261 Å2
Baniso -1Baniso -2Baniso -3
1--0.86 Å2-0 Å20 Å2
2---0.61 Å2-0 Å2
3---1.47 Å2
Refinement stepCycle: 1 / Resolution: 2→20.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2037 0 30 215 2282
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0132123
X-RAY DIFFRACTIONr_bond_other_d0.0030.0142039
X-RAY DIFFRACTIONr_angle_refined_deg1.9411.6482920
X-RAY DIFFRACTIONr_angle_other_deg1.3371.5664686
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6075278
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.50518.49593
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.76515291
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.061522
X-RAY DIFFRACTIONr_chiral_restr0.0910.2273
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022365
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02450
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_it1.3091.6091109
X-RAY DIFFRACTIONr_mcbond_other1.3071.6071108
X-RAY DIFFRACTIONr_mcangle_it1.9832.4061385
X-RAY DIFFRACTIONr_mcangle_other1.9832.4081386
X-RAY DIFFRACTIONr_scbond_it1.7491.8181013
X-RAY DIFFRACTIONr_scbond_other1.7481.8171011
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.7122.6521534
X-RAY DIFFRACTIONr_long_range_B_refined4.23320.0242360
X-RAY DIFFRACTIONr_long_range_B_other4.00519.8252311
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
Rfree0.381 65 -
Rwork0.315 1208 -
obs--95.57 %

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