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- PDB-2gey: Crystal Structure of AclR a putative hydroxylase from Streptomyce... -

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Basic information

Entry
Database: PDB / ID: 2gey
TitleCrystal Structure of AclR a putative hydroxylase from Streptomyces galilaeus
ComponentsAclR protein
KeywordsOXIDOREDUCTASE / alpha+beta barrel
Function / homology
Function and homology information


polyketide metabolic process
Similarity search - Function
SnoaL-like polyketide cyclase / Polyketide cyclase SnoaL-like / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / AclR protein
Similarity search - Component
Biological speciesStreptomyces galilaeus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsBeinker, P. / Lohkamp, B. / Schneider, G.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Crystal structures of SnoaL2 and AclR: two putative hydroxylases in the biosynthesis of aromatic polyketide antibiotics
Authors: Beinker, P. / Lohkamp, B. / Peltonen, T. / Niemi, J. / Mantsala, P. / Schneider, G.
History
DepositionMar 21, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 18, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: AclR protein
B: AclR protein
C: AclR protein
D: AclR protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,15914
Polymers71,8154
Non-polymers1,34310
Water9,872548
1
A: AclR protein
B: AclR protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6788
Polymers35,9082
Non-polymers7716
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint1 kcal/mol
Surface area14360 Å2
MethodPISA
2
C: AclR protein
D: AclR protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4806
Polymers35,9082
Non-polymers5734
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4490 Å2
ΔGint-1 kcal/mol
Surface area13620 Å2
MethodPISA
3
A: AclR protein
B: AclR protein
hetero molecules

C: AclR protein
D: AclR protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,15914
Polymers71,8154
Non-polymers1,34310
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_645-x+1,y-1/2,-z+1/21
Buried area9630 Å2
ΔGint-2 kcal/mol
Surface area27310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.908, 81.724, 136.640
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
AclR protein / putative hydroxylase


Mass: 17953.768 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces galilaeus (bacteria) / Strain: ATCC31133 / Gene: aclr / Plasmid: pET30b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q1XDX7
#2: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 548 / 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: 3.14 Å3/Da / Density % sol: 60.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 18% PEG 400, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.0202 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 15, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0202 Å / Relative weight: 1
ReflectionResolution: 1.8→70.2 Å / Num. all: 82990 / Num. obs: 79308 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 23.7 Å2 / Rsym value: 0.074 / Net I/σ(I): 17.3
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 5 % / Mean I/σ(I) obs: 3 / Rsym value: 0.448 / % possible all: 88.2

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Processing

SoftwareName: REFMAC / Version: 5.2.0005 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GEX

2gex


Resolution: 1.8→43.98 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.797 / SU ML: 0.062 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.099 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19712 4133 5 %RANDOM
Rwork0.17483 ---
all0.17594 78779 --
obs0.17594 78779 98.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.409 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å20 Å2
2--0.18 Å20 Å2
3----0.12 Å2
Refinement stepCycle: LAST / Resolution: 1.8→43.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4558 0 89 548 5195
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0224985
X-RAY DIFFRACTIONr_bond_other_d0.0010.024707
X-RAY DIFFRACTIONr_angle_refined_deg1.0961.9696786
X-RAY DIFFRACTIONr_angle_other_deg0.7113.00210873
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2545651
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.81923.991223
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.30515908
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4971534
X-RAY DIFFRACTIONr_chiral_restr0.0630.2760
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025461
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02961
X-RAY DIFFRACTIONr_nbd_refined0.1970.2926
X-RAY DIFFRACTIONr_nbd_other0.1720.24748
X-RAY DIFFRACTIONr_nbtor_refined0.1670.22313
X-RAY DIFFRACTIONr_nbtor_other0.0820.22964
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1120.2418
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1750.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1970.253
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1370.227
X-RAY DIFFRACTIONr_mcbond_it0.6861.53916
X-RAY DIFFRACTIONr_mcbond_other0.1121.51206
X-RAY DIFFRACTIONr_mcangle_it0.74524855
X-RAY DIFFRACTIONr_scbond_it1.5732267
X-RAY DIFFRACTIONr_scangle_it2.464.51891
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 268 -
Rwork0.228 4890 -
obs--83.63 %
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)
10.3643-0.33630.31870.9135-0.74231.188-0.0215-0.05190.07690.1028-0.102-0.1799-0.08140.20190.1235-0.0989-0.0345-0.0053-0.07650.0302-0.066433.701413.04636.5013
21.87610.2125-0.33271.5633-0.12381.29340.0352-0.387-0.24270.1172-0.1093-0.22760.05220.29110.0742-0.0844-0.0462-0.02610.0160.1095-0.068127.26622.842849.8937
30.9890.2790.33950.98160.17141.36150.01490.16050.0965-0.16680.0097-0.0612-0.11070.0045-0.0245-0.080.0377-0.0141-0.1068-0.0106-0.08681.175235.6721.1444
41.9610.1405-0.06321.11630.03941.24380.04130.2033-0.057-0.1530.0293-0.030.10280.0661-0.0706-0.10210.0181-0.0117-0.1409-0.0172-0.12416.174324.23497.1538
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 1582 - 158
2X-RAY DIFFRACTION2BB2 - 1342 - 134
3X-RAY DIFFRACTION3CC2 - 1512 - 151
4X-RAY DIFFRACTION4DD2 - 1342 - 134

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