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- PDB-3gzb: Crystal structure of putative SnoaL-like polyketide cyclase (YP_0... -

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Entry
Database: PDB / ID: 3gzb
TitleCrystal structure of putative SnoaL-like polyketide cyclase (YP_001182657.1) from Shewanella putrefaciens CN-32 at 1.44 A resolution
ComponentsPutative SnoaL-like polyketide cyclase
KeywordsLYASE / YP_001182657.1 / Putative SnoaL-like polyketide cyclase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homologySnoaL-like domain / SnoaL-like domain / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta / SnoaL-like domain-containing protein
Function and homology information
Biological speciesShewanella putrefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.44 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of putative SnoaL-like polyketide cyclase (YP_001182657.1) from Shewanella putrefaciens CN-32 at 1.44 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionApr 6, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / 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: Putative SnoaL-like polyketide cyclase
B: Putative SnoaL-like polyketide cyclase
C: Putative SnoaL-like polyketide cyclase
D: Putative SnoaL-like polyketide cyclase
E: Putative SnoaL-like polyketide cyclase
F: Putative SnoaL-like polyketide cyclase
G: Putative SnoaL-like polyketide cyclase
H: Putative SnoaL-like polyketide cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,99454
Polymers143,1858
Non-polymers3,80946
Water31,2201733
1
A: Putative SnoaL-like polyketide cyclase
B: Putative SnoaL-like polyketide cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,82815
Polymers35,7962
Non-polymers1,03113
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-12.7 kcal/mol
Surface area15410 Å2
MethodPISA
2
C: Putative SnoaL-like polyketide cyclase
D: Putative SnoaL-like polyketide cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,64112
Polymers35,7962
Non-polymers84510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1380 Å2
ΔGint-12.1 kcal/mol
Surface area15360 Å2
MethodPISA
3
E: Putative SnoaL-like polyketide cyclase
F: Putative SnoaL-like polyketide cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,82214
Polymers35,7962
Non-polymers1,02512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1320 Å2
ΔGint-12.6 kcal/mol
Surface area15440 Å2
MethodPISA
4
G: Putative SnoaL-like polyketide cyclase
H: Putative SnoaL-like polyketide cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,70313
Polymers35,7962
Non-polymers90711
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-12.4 kcal/mol
Surface area15320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.240, 89.940, 94.320
Angle α, β, γ (deg.)90.000, 89.940, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21D
31F
41H
12A
22C
32E
42G

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115B0 - 153
2115D0 - 153
3115F0 - 153
4115H0 - 153
1125A0 - 153
2125C0 - 153
3125E0 - 153
4125G0 - 153

NCS ensembles :
ID
1
2

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Components

#1: Protein
Putative SnoaL-like polyketide cyclase


Mass: 17898.113 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella putrefaciens (bacteria) / Strain: CN-32 / Gene: Sputcn32_1130, YP_001182657.1 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: A4Y4H5
#2: Chemical
ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 29 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1733 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 2.67 Å3/Da / Density % sol: 53.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.64
Details: NANODROP, 17.70% 2-methyl-2,4-pentanediol, 0.1M HEPES pH 6.64, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL11-110.91837
SYNCHROTRONSSRL BL11-120.97845
Detector
TypeIDDetectorDateDetails
MARMOSAIC 325 mm CCD1CCDFeb 23, 2009Flat mirror (vertical focusing)
MARMOSAIC 325 mm CCD2CCDFeb 18, 2009Flat mirror (vertical focusing)
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Single crystal Si(111) bent (horizontal focusing)SINGLE WAVELENGTHMx-ray1
2Single crystal Si(111) bent (horizontal focusing)SADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.978451
ReflectionResolution: 1.44→47.14 Å / Num. obs: 269676 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 17.07 Å2 / Rmerge(I) obs: 0.063
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.44-1.520.4992120097401551,299.1
1.52-1.580.323.176688251351,299.4
1.58-1.660.244.287003281181,299.6
1.66-1.740.1765.672328232741,299.7
1.74-1.850.137.380011257081,299.6
1.85-1.990.0969.877653250141,299.6
1.99-2.20.07412.681530265621,299.1
2.2-2.510.08317.5130722247621,299.5
2.51-3.160.06422.2154951254841,299.2
3.16-47.140.04728.1152339254641,297.6

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0053refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
MAR345CCDdata collection
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.44→47.14 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.968 / Occupancy max: 1 / Occupancy min: 0.15 / SU B: 2.145 / SU ML: 0.037 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.053 / ESU R Free: 0.056
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 4. MPD/MRD AND EDO MODELED ARE PRESENT IN CRYSTALLIZATION/CRYO CONDITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.174 13577 5 %RANDOM
Rwork0.151 ---
obs0.152 269639 99.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 63.64 Å2 / Biso mean: 17.385 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.65 Å20 Å20.4 Å2
2---0.42 Å20 Å2
3---1.08 Å2
Refinement stepCycle: LAST / Resolution: 1.44→47.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9355 0 252 1733 11340
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02210563
X-RAY DIFFRACTIONr_bond_other_d0.0010.027369
X-RAY DIFFRACTIONr_angle_refined_deg1.6081.9714356
X-RAY DIFFRACTIONr_angle_other_deg0.902318020
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.86551379
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.34424.133542
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.898151940
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.531568
X-RAY DIFFRACTIONr_chiral_restr0.1020.21538
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211776
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022216
X-RAY DIFFRACTIONr_mcbond_it1.57636126
X-RAY DIFFRACTIONr_mcbond_other0.47432480
X-RAY DIFFRACTIONr_mcangle_it2.542510012
X-RAY DIFFRACTIONr_scbond_it4.15284437
X-RAY DIFFRACTIONr_scangle_it6.122114227
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A790MEDIUM POSITIONAL0.130.5
1B790MEDIUM POSITIONAL0.090.5
1C790MEDIUM POSITIONAL0.140.5
1D790MEDIUM POSITIONAL0.10.5
1A942LOOSE POSITIONAL0.415
1B942LOOSE POSITIONAL0.385
1C942LOOSE POSITIONAL0.365
1D942LOOSE POSITIONAL0.365
1A790MEDIUM THERMAL1.712
1B790MEDIUM THERMAL2.132
1C790MEDIUM THERMAL2.462
1D790MEDIUM THERMAL1.662
1A942LOOSE THERMAL1.9210
1B942LOOSE THERMAL2.1410
1C942LOOSE THERMAL2.3410
1D942LOOSE THERMAL1.7410
2A887MEDIUM POSITIONAL0.150.5
2B887MEDIUM POSITIONAL0.120.5
2C887MEDIUM POSITIONAL0.090.5
2D887MEDIUM POSITIONAL0.090.5
2A1060LOOSE POSITIONAL0.395
2B1060LOOSE POSITIONAL0.335
2C1060LOOSE POSITIONAL0.475
2D1060LOOSE POSITIONAL0.495
2A887MEDIUM THERMAL2.752
2B887MEDIUM THERMAL2.542
2C887MEDIUM THERMAL2.052
2D887MEDIUM THERMAL2.082
2A1060LOOSE THERMAL2.3310
2B1060LOOSE THERMAL2.4310
2C1060LOOSE THERMAL1.9110
2D1060LOOSE THERMAL2.1310
LS refinement shellResolution: 1.44→1.477 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 1013 -
Rwork0.316 18840 -
all-19853 -
obs--98.77 %
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)
10.72680.13320.07340.8746-0.12810.3131-0.0160.00480.0763-0.0588-0.0057-0.1117-0.0112-0.01260.02170.0214-0.00130.00770.00780.00290.02715.674217.475886.8053
20.70460.3016-0.10261.0599-0.07280.3155-0.0269-0.0512-0.0588-0.03840.02730.07940.0257-0.029-0.00050.0324-0.00690.00290.02050.01020.0174-4.46482.777496.4458
30.24020.12940.06860.9746-0.00390.19380.02930.0294-0.0884-0.0698-0.0114-0.00430.01020.0106-0.01790.01780.00560.00420.0046-0.01330.096329.6847-19.494587.3048
41.04520.23330.12960.81660.41460.3651-0.0361-0.0480.01990.01510.0238-0.06710.01050.04310.01240.0244-0.001-0.00570.01120.00920.108749.8745-4.09896.0721
50.8141-0.19450.04510.2132-0.0120.24250.0040.08470.0946-0.00610.00810.03020.0098-0.0243-0.01210.005-0.00050.00520.03540.00490.057-40.8777-9.6162134.3034
60.7432-0.36210.09460.7423-0.00820.3205-0.0049-0.0410.00810.03570.01240.02860.0362-0.0233-0.00740.00820.00010.0030.0238-0.00810.0104-25.6239-29.6845143.3092
70.6676-0.1178-0.01830.5912-0.0180.3164-0.0140.0419-0.10130.0060.00280.0192-0.00770.0150.01120.0171-0.00110.01040.0411-0.00120.0204-3.73914.3078134.3868
81.1437-0.4249-0.25280.94240.1710.49010.00950.01710.05360.0324-0.03530.0742-0.0597-0.00680.02580.01580.00530.00490.039500.0192-19.104924.3818143.4627
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 153
2X-RAY DIFFRACTION2B17 - 153
3X-RAY DIFFRACTION3C0 - 153
4X-RAY DIFFRACTION4D17 - 153
5X-RAY DIFFRACTION5E0 - 153
6X-RAY DIFFRACTION6F17 - 153
7X-RAY DIFFRACTION7G0 - 153
8X-RAY DIFFRACTION8H17 - 153

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