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Basic information

Entry
Database: PDB / ID: 5ag3
TitleChorismatase mechanisms reveal fundamentally different types of reaction in a single conserved protein fold
ComponentsPUTATIVE PTERIDINE-DEPENDENT DIOXYGENASE
KeywordsOXIDOREDUCTASE / PROTEIN
Function / homology3-hydroxybenzoate synthase / Chorismatase, FkbO/Hyg5 family / oxo-acid-lyase activity / RutC-like superfamily / 3-(2-CARBOXYETHYL)BENZOIC ACID / DI(HYDROXYETHYL)ETHER / 3-hydroxybenzoate synthase
Function and homology information
Biological speciesSTREPTOMYCES HYGROSCOPICUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.898 Å
AuthorsHubrich, F. / Juneja, P. / Mueller, M. / Diederichs, K. / Welte, W. / Andexer, J.N.
CitationJournal: J.Am.Chem.Soc. / Year: 2015
Title: Chorismatase Mechanisms Reveal Fundamentally Different Types of Reaction in a Single Conserved Protein Fold.
Authors: Hubrich, F. / Juneja, P. / Mueller, M. / Diederichs, K. / Welte, W. / Andexer, J.N.
History
DepositionJan 28, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 19, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2015Group: Database references
Revision 1.2Aug 23, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.3Jan 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 / 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 / _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: PUTATIVE PTERIDINE-DEPENDENT DIOXYGENASE
B: PUTATIVE PTERIDINE-DEPENDENT DIOXYGENASE
C: PUTATIVE PTERIDINE-DEPENDENT DIOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,65823
Polymers112,4103
Non-polymers2,24820
Water11,656647
1
A: PUTATIVE PTERIDINE-DEPENDENT DIOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,59911
Polymers37,4701
Non-polymers1,12910
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PUTATIVE PTERIDINE-DEPENDENT DIOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9735
Polymers37,4701
Non-polymers5024
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: PUTATIVE PTERIDINE-DEPENDENT DIOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0877
Polymers37,4701
Non-polymers6176
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)116.175, 116.175, 70.429
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein PUTATIVE PTERIDINE-DEPENDENT DIOXYGENASE / HYG5-CHORISMATASE


Mass: 37470.043 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOMYCES HYGROSCOPICUS (bacteria) / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RP-PL1SL2 / References: UniProt: O30478
#2: Chemical ChemComp-3EB / 3-(2-CARBOXYETHYL)BENZOIC ACID


Mass: 194.184 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H10O4
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 647 / 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: 2.39 Å3/Da / Density % sol: 48.6 % / Description: NONE
Crystal growpH: 6.5
Details: HYG5 WAS CONCENTRATED TO 2.5 TO 3 MG/ML AND AFTERWARDS SUPPLEMENTED WITH 15 MM 3-2-CARBOXYETHYL-BENZOATE EQUILIBRATION AGAINST A RESERVOIR SOLUTION OF 0.1 M MES PH 6.5, 0.2 M AMMONIUM ...Details: HYG5 WAS CONCENTRATED TO 2.5 TO 3 MG/ML AND AFTERWARDS SUPPLEMENTED WITH 15 MM 3-2-CARBOXYETHYL-BENZOATE EQUILIBRATION AGAINST A RESERVOIR SOLUTION OF 0.1 M MES PH 6.5, 0.2 M AMMONIUM SULFATE AND 20 TO 25 PERCENT PEG 5000 MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.0001
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 12, 2013 / Details: DYNAMICALLY BENDABLE MIRROR
RadiationMonochromator: LN2 COOLED FIXED-EXIT SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0001 Å / Relative weight: 1
Reflection twinOperator: -h,-k,l / Fraction: 0.5
ReflectionResolution: 1.9→50 Å / Num. obs: 83807 / % possible obs: 99.8 % / Observed criterion σ(I): 0.92 / Redundancy: 5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.5
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 0.88 / % possible all: 98.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4BPS

4bps


Resolution: 1.898→44.812 Å / σ(F): 1.94 / Phase error: 20.09 / Stereochemistry target values: TWIN_LSQ_F
Details: AMINO ACID AT N TERMINAL AMINO ACID ARE NOT BUILD CHAIN A- 1-7 CHAIN B- 1-8 CHAIN C - 1-5
RfactorNum. reflection% reflection
Rfree0.1845 4186 5 %
Rwork0.1494 --
obs0.1562 83807 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.898→44.812 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7768 0 144 647 8559
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098089
X-RAY DIFFRACTIONf_angle_d1.32810950
X-RAY DIFFRACTIONf_dihedral_angle_d14.2412937
X-RAY DIFFRACTIONf_chiral_restr0.0531149
X-RAY DIFFRACTIONf_plane_restr0.0061476
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.93280.32232020.28393961X-RAY DIFFRACTION95
1.9328-1.96790.2952140.27443988X-RAY DIFFRACTION95
1.9679-2.00580.27092090.25673973X-RAY DIFFRACTION95
2.0058-2.04670.29042050.24753960X-RAY DIFFRACTION95
2.0467-2.09120.29082220.23873976X-RAY DIFFRACTION95
2.0912-2.13980.28942130.22583965X-RAY DIFFRACTION95
2.1398-2.19340.22612120.21584061X-RAY DIFFRACTION95
2.1934-2.25270.21732130.20713919X-RAY DIFFRACTION95
2.2527-2.31890.26011990.19713989X-RAY DIFFRACTION95
2.3189-2.39380.22432110.19613950X-RAY DIFFRACTION95
2.3938-2.47930.22072240.18954006X-RAY DIFFRACTION95
2.4793-2.57860.21071850.18413975X-RAY DIFFRACTION96
2.5786-2.69590.21492400.1773962X-RAY DIFFRACTION94
2.6959-2.8380.20732220.16733981X-RAY DIFFRACTION95
2.838-3.01580.19531830.16623975X-RAY DIFFRACTION96
3.0158-3.24850.18462050.15773992X-RAY DIFFRACTION95
3.2485-3.57530.18231970.1384013X-RAY DIFFRACTION95
3.5753-4.09220.16422080.12163964X-RAY DIFFRACTION95
4.0922-5.15410.1282000.09443983X-RAY DIFFRACTION95
5.1541-40.94490.1472200.11693974X-RAY DIFFRACTION95
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)
12.5941-0.4087-1.26244.5389-0.82022.84450.0839-0.4753-0.3170.51380.0496-0.2719-0.00760.3119-0.23490.22310.034-0.04610.28720.04380.2588-12.0949-13.612914.4616
21.2364-0.1347-0.29490.8012-0.07071.45170.10730.1985-0.1161-0.1498-0.06660.04870.0462-0.0481-0.04560.18510.0455-0.02460.2187-0.01320.2056-16.4886-7.3682-3.4792
32.91590.20050.24543.9387-0.41411.5801-0.0537-0.0298-0.11820.19550.12130.25160.0164-0.2044-0.06990.16740.06480.02120.2475-0.01460.1964-28.64480.33848.4946
43.1133-0.40520.31775.055-0.4543.9278-0.1569-0.33320.37480.53640.04260.1499-0.4408-0.06840.0740.21280.02650.00750.2487-0.03830.3014-47.9686-22.7198-23.453
50.9977-0.79070.04214.26431.73473.6099-0.03170.13870.1409-0.2777-0.00260.1279-0.26550.04290.0420.15720.00140.00630.2250.01320.2401-42.2108-27.1516-40.8209
63.00370.3121.10592.57661.49893.5903-0.04710.00530.0167-0.20820.0941-0.2867-0.08530.4186-0.01690.17110.03480.0580.2590.04950.2371-30.5307-29.356-39.009
72.88450.80680.05723.15440.24281.7862-0.0899-0.2942-0.03440.2890.0232-0.1490.04710.25620.08240.21990.0956-0.02240.31960.02480.2219-29.6499-36.2254-25.7461
81.2680.43980.48681.31960.5742.190.040.05760.0628-0.0849-0.0345-0.0193-0.14210.0226-0.01240.1630.04340.01780.15950.02050.2201-41.231331.2007-36.5766
94.2411-1.5962-1.18744.5183-0.62064.3245-0.18340.7548-0.1468-0.85990.26810.04060.40250.0752-0.04470.341-0.01680.01670.2920.01250.2625-30.552718.3625-36.232
105.24720.77491.08111.54260.53421.11430.13670.026-0.42970.0898-0.0556-0.01980.16370.0178-0.07820.18910.0094-0.00090.15040.05050.2401-39.200112.6939-26.5076
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 8 THROUGH 37 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 38 THROUGH 220 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 221 THROUGH 340 )
4X-RAY DIFFRACTION4CHAIN 'B' AND (RESID 9 THROUGH 79 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 80 THROUGH 180 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 181 THROUGH 224 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 225 THROUGH 340 )
8X-RAY DIFFRACTION8CHAIN 'C' AND (RESID 6 THROUGH 196 )
9X-RAY DIFFRACTION9CHAIN 'C' AND (RESID 197 THROUGH 243 )
10X-RAY DIFFRACTION10CHAIN 'C' AND (RESID 244 THROUGH 340 )

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