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- PDB-4v1y: The structure of the hexameric atrazine chlorohydrolase, AtzA -

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Basic information

Entry
Database: PDB / ID: 4v1y
TitleThe structure of the hexameric atrazine chlorohydrolase, AtzA
ComponentsATRAZINE CHLOROHYDROLASE
KeywordsHYDROLASE / BIOREMEDIATION / PROTEIN EVOLUTION / DEHALOGENASE
Function / homology
Function and homology information


atrazine chlorohydrolase / atrazine chlorohydrolase activity / atrazine catabolic process / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / metal ion binding / cytoplasm
Similarity search - Function
Urease, subunit C; domain 1 / Urease, subunit C, domain 1 / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolases / Metal-dependent hydrolase / Roll / TIM Barrel / Alpha-Beta Barrel ...Urease, subunit C; domain 1 / Urease, subunit C, domain 1 / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolases / Metal-dependent hydrolase / Roll / TIM Barrel / Alpha-Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / DI(HYDROXYETHYL)ETHER / Atrazine chlorohydrolase
Similarity search - Component
Biological speciesPSEUDOMONAS SP. ADP (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsPeat, T.S. / Newman, J. / Balotra, S. / Lucent, D. / Warden, A.C. / Scott, C.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: The Structure of the Hexameric Atrazine Chlorohydrolase Atza.
Authors: Peat, T.S. / Newman, J. / Balotra, S. / Lucent, D. / Warden, A.C. / Scott, C.
History
DepositionOct 4, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 11, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATRAZINE CHLOROHYDROLASE
B: ATRAZINE CHLOROHYDROLASE
C: ATRAZINE CHLOROHYDROLASE
D: ATRAZINE CHLOROHYDROLASE
E: ATRAZINE CHLOROHYDROLASE
F: ATRAZINE CHLOROHYDROLASE
G: ATRAZINE CHLOROHYDROLASE
H: ATRAZINE CHLOROHYDROLASE
I: ATRAZINE CHLOROHYDROLASE
J: ATRAZINE CHLOROHYDROLASE
K: ATRAZINE CHLOROHYDROLASE
L: ATRAZINE CHLOROHYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)658,88244
Polymers656,68912
Non-polymers2,19332
Water2,900161
1
A: ATRAZINE CHLOROHYDROLASE
B: ATRAZINE CHLOROHYDROLASE
C: ATRAZINE CHLOROHYDROLASE
D: ATRAZINE CHLOROHYDROLASE
E: ATRAZINE CHLOROHYDROLASE
F: ATRAZINE CHLOROHYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)329,47622
Polymers328,3446
Non-polymers1,13216
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32950 Å2
ΔGint-126.6 kcal/mol
Surface area102460 Å2
MethodPISA
2
G: ATRAZINE CHLOROHYDROLASE
H: ATRAZINE CHLOROHYDROLASE
I: ATRAZINE CHLOROHYDROLASE
J: ATRAZINE CHLOROHYDROLASE
K: ATRAZINE CHLOROHYDROLASE
L: ATRAZINE CHLOROHYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)329,40622
Polymers328,3446
Non-polymers1,06116
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33380 Å2
ΔGint-133 kcal/mol
Surface area102660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.487, 195.564, 283.882
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

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Protein , 1 types, 12 molecules ABCDEFGHIJKL

#1: Protein
ATRAZINE CHLOROHYDROLASE


Mass: 54724.082 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Details: N-TERMINAL HIS-TAG TO AID PURIFICATION. / Source: (gene. exp.) PSEUDOMONAS SP. ADP (bacteria) / Plasmid: PETCC2 / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / References: UniProt: P72156, atrazine chlorohydrolase

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Non-polymers , 5 types, 193 molecules

#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsN-TERMINAL HIS-TAG ADDED TO AID IN PURIFICATION

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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: 2.56 Å3/Da / Density % sol: 56 % / Description: NONE
Crystal growpH: 7.1
Details: THE PROTEIN WAS CONCENTRATED TO 11.4 MG/ML AND SET UP IN A 1:1 RATIO, 150 NL PLUS 150 NL, WITH 50 MM HEPES PH 7.1, 2.7% DIETHYLENE GLYCOL, 5.5% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537
DetectorType: ADSC CCD / Detector: CCD / Date: May 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.8→49.5 Å / Num. obs: 161122 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Rmerge(I) obs: 0.23 / Net I/σ(I): 8.8
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.91 / Mean I/σ(I) obs: 2.6 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3HPA

3hpa


Resolution: 2.8→161.05 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.899 / SU B: 29.01 / SU ML: 0.252 / Cross valid method: THROUGHOUT / ESU R Free: 0.336 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED TWO FULL HEXAMERS ARE FOUND IN THE ASYMMETRIC UNIT.
RfactorNum. reflection% reflectionSelection details
Rfree0.21794 7864 4.9 %RANDOM
Rwork0.18742 ---
obs0.1889 153180 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.473 Å2
Baniso -1Baniso -2Baniso -3
1--1.3 Å20 Å20 Å2
2---1.42 Å20 Å2
3---2.72 Å2
Refinement stepCycle: LAST / Resolution: 2.8→161.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms44161 0 110 161 44432
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01945661
X-RAY DIFFRACTIONr_bond_other_d0.0020.0243532
X-RAY DIFFRACTIONr_angle_refined_deg1.5051.93862016
X-RAY DIFFRACTIONr_angle_other_deg2399453
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.56955765
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.23422.9552200
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.441157447
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.99715463
X-RAY DIFFRACTIONr_chiral_restr0.0790.26886
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02152690
X-RAY DIFFRACTIONr_gen_planes_other0.0040.0210977
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_it1.6652.08622955
X-RAY DIFFRACTIONr_mcbond_other1.6652.08622954
X-RAY DIFFRACTIONr_mcangle_it2.7613.12528755
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.4032.41222706
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 544 -
Rwork0.271 11246 -
obs--99.99 %
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)
10.247-0.08920.1370.2641-0.11980.3471-0.0063-0.0413-0.07610.05510.04880.07080.0918-0.0615-0.04250.0828-0.03110.00330.05260.03980.048134.007837.024448.0508
20.2611-0.1038-0.04360.2830.14110.36210.04560.02360.0027-0.0035-0.03350.0588-0.0132-0.0131-0.01210.0387-0.0053-0.01270.0530.00460.0447132.790562.037925.3157
30.3323-0.1084-0.2150.4490.0880.4292-0.0066-0.045-0.04790.1369-0.0472-0.2478-0.01950.04590.05370.0665-0.0165-0.09450.0180.04690.1807189.839826.636944.3961
40.17240.0280.04060.6104-0.20870.261-0.00150.0295-0.0615-0.0672-0.037-0.07010.0409-0.0290.03850.09960.01570.0080.0294-0.00320.0772169.870118.924418.18
50.21550.00840.050.3747-0.14010.14060.0228-0.02140.02790.1304-0.0223-0.0557-0.0239-0.0219-0.00050.1099-0.0213-0.04210.03110.00720.0295171.049280.064951.8747
60.3930.07850.10460.15090.12470.34120.01980.05580.0109-0.02290.0148-0.11860.0370.0162-0.03460.0252-0.00980.02320.02790.02140.1407188.961472.249824.1759
70.2376-0.0440.21850.5157-0.0120.44340.034-0.0461-0.07330.01640.01580.03570.07890.0022-0.04980.0779-0.0287-0.00840.03290.01440.0475124.578118.3051-15.4857
80.26360.0075-0.10390.3332-0.09590.43520.0362-0.0043-0.0807-0.1470.00940.16020.0262-0.0936-0.04560.0853-0.0267-0.07940.05470.00750.108104.384625.0654-41.7835
90.24290.1461-0.03810.2534-0.06950.20790.0528-0.0373-0.0085-0.0099-0.046-0.05190.00070.0014-0.00680.04960.0053-0.00380.0530.01150.0465161.433461.1568-24.0888
100.17670.06810.10140.3393-0.02570.27670.0140.0423-0.083-0.0431-0.0046-0.09130.0307-0.0032-0.00940.08320.02540.01740.0226-0.0180.0636160.149735.4308-46.0011
110.3828-0.07890.06470.2043-0.10540.22350.0216-0.07990.02150.0350.01460.07010.0329-0.0535-0.03630.0295-0.0020.00910.0675-0.01240.0568105.165271.3468-23.0245
120.21720.0447-0.00470.25540.07740.18280.00730.05060.0395-0.07410.01460.0138-0.02360.0121-0.0220.07320.0134-0.01220.0590.00280.0296122.975778.2142-51.0198
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 481
2X-RAY DIFFRACTION2B1 - 481
3X-RAY DIFFRACTION3C2 - 481
4X-RAY DIFFRACTION4D1 - 481
5X-RAY DIFFRACTION5E1 - 481
6X-RAY DIFFRACTION6F1 - 481
7X-RAY DIFFRACTION7G1 - 481
8X-RAY DIFFRACTION8H3 - 481
9X-RAY DIFFRACTION9I1 - 481
10X-RAY DIFFRACTION10J2 - 481
11X-RAY DIFFRACTION11K1 - 481
12X-RAY DIFFRACTION12L1 - 481

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