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- PDB-3kl2: Crystal structure of a putative isochorismatase from Streptomyces... -

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Basic information

Entry
Database: PDB / ID: 3kl2
TitleCrystal structure of a putative isochorismatase from Streptomyces avermitilis
ComponentsPutative isochorismatase
Keywordsstructural genomics / unknown function / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homologyIsochorismatase-like / Isochorismatase-like / Isochorismatase-like superfamily / Isochorismatase family / catalytic activity / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Putative isochorismatase
Function and homology information
Biological speciesStreptomyces avermitilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsBonanno, J.B. / Dickey, M. / Bain, K.T. / Chang, S. / Ozyurt, S. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of a putative isochorismatase from Streptomyces avermitilis
Authors: Bonanno, J.B. / Dickey, M. / Bain, K.T. / Chang, S. / Ozyurt, S. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionNov 6, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Nov 21, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)291,43914
Polymers291,24712
Non-polymers1922
Water3,135174
1
A: Putative isochorismatase
B: Putative isochorismatase
C: Putative isochorismatase
D: Putative isochorismatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,1785
Polymers97,0824
Non-polymers961
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9100 Å2
ΔGint-49 kcal/mol
Surface area26510 Å2
MethodPISA
2
E: Putative isochorismatase
F: Putative isochorismatase
G: Putative isochorismatase
H: Putative isochorismatase


Theoretical massNumber of molelcules
Total (without water)97,0824
Polymers97,0824
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9090 Å2
ΔGint-23 kcal/mol
Surface area27240 Å2
MethodPISA
3
I: Putative isochorismatase
J: Putative isochorismatase
K: Putative isochorismatase
L: Putative isochorismatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,1785
Polymers97,0824
Non-polymers961
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8910 Å2
ΔGint-37 kcal/mol
Surface area26930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.742, 112.102, 178.904
Angle α, β, γ (deg.)90.000, 99.470, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Putative isochorismatase


Mass: 24270.561 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces avermitilis (bacteria) / Gene: dhbB1, SAV1388, SAV_1388 / Plasmid: modified pET26 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q82NB5
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 2.3 Å3/Da / Density % sol: 46.54 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 7
Details: 35% PEG 8K, 250mM ammonium sulfate, pH 7.0, vapor diffusion, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97958 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 8, 2009
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97958 Å / Relative weight: 1
ReflectionResolution: 2.3→39.962 Å / Num. all: 117040 / Num. obs: 114465 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 36 Å2 / Rmerge(I) obs: 0.099 / Rsym value: 0.099 / Net I/σ(I): 9.3
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.407 / Mean I/σ(I) obs: 2.9 / Num. unique all: 16523 / Rsym value: 0.407 / % possible all: 96.9

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Processing

Software
NameVersionClassificationNB
SCALA3.3.9data scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
MAR345CCDdata collection
MOSFLMdata reduction
SHELXCDphasing
SHELXEmodel building
MLPHAREphasing
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.923 / WRfactor Rfree: 0.24 / WRfactor Rwork: 0.189 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.85 / SU B: 15.384 / SU ML: 0.168 / SU R Cruickshank DPI: 0.311 / SU Rfree: 0.23 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.311 / ESU R Free: 0.23 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.239 5723 5 %RANDOM
Rwork0.188 ---
obs0.191 114268 97.73 %-
all-116922 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 67.47 Å2 / Biso mean: 21.314 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--1.65 Å20 Å21.15 Å2
2--4.19 Å20 Å2
3----2.16 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17773 0 10 174 17957
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02218104
X-RAY DIFFRACTIONr_bond_other_d0.0010.0211467
X-RAY DIFFRACTIONr_angle_refined_deg1.5141.95124657
X-RAY DIFFRACTIONr_angle_other_deg0.952328092
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.24652395
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.60324.128717
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.712152753
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2541591
X-RAY DIFFRACTIONr_chiral_restr0.0850.22947
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0220560
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023631
X-RAY DIFFRACTIONr_mcbond_it0.6791.511866
X-RAY DIFFRACTIONr_mcbond_other0.1651.54959
X-RAY DIFFRACTIONr_mcangle_it1.261219037
X-RAY DIFFRACTIONr_scbond_it2.24536238
X-RAY DIFFRACTIONr_scangle_it3.5584.55620
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 379 -
Rwork0.248 7798 -
all-8177 -
obs-7798 96.35 %
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)
11.64470.08380.34351.11030.28681.8003-0.00710.17420.1798-0.0107-0.0243-0.0236-0.0582-0.22010.03140.03870.022-0.00270.08350.04670.1155-46.4219.21465.966
22.341-0.044-0.44321.0003-0.02621.57020.0014-0.31580.19080.01630.0176-0.0134-0.0372-0.2279-0.01910.00760.0048-0.0140.1677-0.02760.053-50.63-1.5690.122
32.151-0.0151-0.31971.0635-0.11671.4332-0.02940.18660.0689-0.07140.01740.01180.02060.10670.0120.03080.0182-0.00320.0934-0.01330.012-22.623-8.85366.611
42.3367-0.14180.08371.6297-0.26372.4448-0.0133-0.18550.17110.04130.01310.00140.05450.25540.00030.0050.0194-0.00810.1025-0.05090.0357-20.9441.12191.606
52.16910.1443-0.54010.984-0.08252.4324-0.02760.16260.1613-0.0550.0679-0.0255-0.0059-0.174-0.04020.023-0.0299-0.01780.05810.0330.0294-40.2561.30227.7
61.96490.0116-0.08171.6021-0.73561.26860.07880.24120.2299-0.13440.00580.1546-0.1023-0.2499-0.08450.09360.0113-0.01570.23560.11380.1848-38.22320.8559.19
71.81210.1345-0.09161.3484-0.42121.86460.0211-0.06810.1435-0.0064-0.0752-0.0541-0.01580.15630.0540.0458-0.0399-0.01490.08230.00690.068-12.90511.71934.572
81.73560.2156-0.58421.9735-0.34071.97810.00760.07380.14810.027-0.0576-0.05930.00960.08540.05010.0429-0.0106-0.00760.1190.07710.0572-10.38710.4097.967
91.45040.1718-0.20181.5503-0.03561.8401-0.161-0.0096-0.30730.07430.0302-0.16070.43360.1820.13070.25330.08890.07950.08850.05620.23211.992-1.79-24.44
102.86310.4847-0.66191.41830.35211.6975-0.34270.3992-0.5451-0.12290.0911-0.23980.35810.02170.25160.2885-0.06470.1660.1603-0.10390.2356-5.033-1.198-50.212
111.74010.09030.39831.1080.292.7578-0.05610.042-0.0548-0.0264-0.0077-0.0411-0.08160.12360.06390.07320.01780.02350.02120.02180.0306-9.46725.569-25.197
122.32520.4147-0.11381.2873-0.05742.5053-0.19020.1454-0.0723-0.09830.13420.0384-0.17940.07850.05610.139-0.04360.01740.08630.01840.01985.22926.671-47.824
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A37 - 235
2X-RAY DIFFRACTION2B37 - 236
3X-RAY DIFFRACTION3C37 - 236
4X-RAY DIFFRACTION4D37 - 236
5X-RAY DIFFRACTION5E36 - 239
6X-RAY DIFFRACTION6F36 - 236
7X-RAY DIFFRACTION7G37 - 236
8X-RAY DIFFRACTION8H36 - 235
9X-RAY DIFFRACTION9I37 - 235
10X-RAY DIFFRACTION10J37 - 235
11X-RAY DIFFRACTION11K37 - 236
12X-RAY DIFFRACTION12L37 - 236

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