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- PDB-3czb: Crystal structure of putative transglycosylase from Caulobacter c... -

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Basic information

Entry
Database: PDB / ID: 3czb
TitleCrystal structure of putative transglycosylase from Caulobacter crescentus
ComponentsPutative transglycosylase
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


: / lytic transglycosylase activity / peptidoglycan turnover / outer membrane / hydrolase activity, hydrolyzing O-glycosyl compounds / peptidoglycan catabolic process / cell wall organization
Similarity search - Function
Barwin-like endoglucanases / Lytic transglycosylase MltA, domain B / Membrane-bound lytic murein transglycosylase A / MltA specific insert domain / MltA specific insert domain / 3D domain / 3D domain / RlpA-like domain / RlpA-like domain superfamily / Ribosomal Protein L25; Chain P ...Barwin-like endoglucanases / Lytic transglycosylase MltA, domain B / Membrane-bound lytic murein transglycosylase A / MltA specific insert domain / MltA specific insert domain / 3D domain / 3D domain / RlpA-like domain / RlpA-like domain superfamily / Ribosomal Protein L25; Chain P / Barwin-like endoglucanases / Prokaryotic membrane lipoprotein lipid attachment site profile. / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
peptidoglycan lytic exotransglycosylase
Similarity search - Component
Biological speciesCaulobacter crescentus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsRamagopal, U.A. / Chattopadhyay, K. / Toro, R. / Wasserman, S. / Freeman, J. / Logan, C. / Bain, K. / Gheyi, T. / Sauder, J.M. / Burley, S.K. ...Ramagopal, U.A. / Chattopadhyay, K. / Toro, R. / Wasserman, S. / Freeman, J. / Logan, C. / Bain, K. / Gheyi, T. / 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 putative transglycosylase from Caulobacter crescentus.
Authors: Ramagopal, U.A. / Chattopadhyay, K. / Toro, R. / Wasserman, S. / Freeman, J. / Logan, C. / Bain, K. / Gheyi, T. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionApr 28, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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 transglycosylase
B: Putative transglycosylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,3359
Polymers74,6632
Non-polymers6727
Water2,954164
1
A: Putative transglycosylase
hetero molecules

B: Putative transglycosylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,3359
Polymers74,6632
Non-polymers6727
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z+2/31
Buried area1570 Å2
ΔGint-16 kcal/mol
Surface area30890 Å2
MethodPISA
2
A: Putative transglycosylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5243
Polymers37,3311
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Putative transglycosylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8126
Polymers37,3311
Non-polymers4805
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)129.604, 129.604, 88.740
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
DetailsAUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

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Components

#1: Protein Putative transglycosylase


Mass: 37331.414 Da / Num. of mol.: 2 / Fragment: Residues 56-395
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caulobacter crescentus (bacteria) / Strain: CB15 / Gene: CC_3740 / Plasmid: BC-pSGX4(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9A226
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.88 Å3/Da / Density % sol: 57.31 %
Description: The structure factor file contains Friedel pairs
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.1M Hepes pH 7.5, 4% 2,2,2-Trifluoroethanol, 1.6M Lithium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 31-ID10.979
SYNCHROTRONAPS 24-ID-C20.979
Detector
TypeIDDetectorDate
MAR CCD 165 mm1CCDApr 1, 2008
ADSC QUANTUM 3152CCDApr 5, 2008
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionRedundancy: 22.5 % / Av σ(I) over netI: 6.2 / Number: 678563 / Rmerge(I) obs: 0.108 / Χ2: 0.96 / D res high: 2.5 Å / D res low: 50 Å / Num. obs: 30161 / % possible obs: 99.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.385099.210.072.47420.8
4.275.3810010.0681.66522.4
3.734.2710010.0741.24822.6
3.393.7310010.0940.9222.7
3.153.3910010.1260.70622.8
2.963.1510010.1870.60122.8
2.822.9610010.2740.55422.8
2.692.8210010.4110.51622.8
2.592.6910010.6050.49822.7
2.52.5910010.8150.47722.6
ReflectionResolution: 2.5→50 Å / Num. all: 30161 / Num. obs: 30161 / % possible obs: 99.9 % / Redundancy: 22.5 % / Rmerge(I) obs: 0.108 / Χ2: 0.961 / Net I/σ(I): 6.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.5-2.5922.60.81529510.4771,2100
2.59-2.6922.70.60530030.4981,2100
2.69-2.8222.80.41129780.5161,2100
2.82-2.9622.80.27429920.5541,2100
2.96-3.1522.80.18730140.6011,2100
3.15-3.3922.80.12629800.7061,2100
3.39-3.7322.70.09430210.921,2100
3.73-4.2722.60.07430141.2481,2100
4.27-5.3822.40.06830671.6651,2100
5.38-5020.80.0731412.4741,299.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL2Mapphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→30.43 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.915 / SU B: 8.618 / SU ML: 0.193 / Cross valid method: THROUGHOUT / ESU R: 0.397 / ESU R Free: 0.268 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: The Friedel pairs were used in phasing
RfactorNum. reflection% reflectionSelection details
Rfree0.25 1544 5.1 %RANDOM
Rwork0.199 ---
obs0.202 30123 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.037 Å2
Baniso -1Baniso -2Baniso -3
1-0.79 Å20.4 Å20 Å2
2--0.79 Å20 Å2
3----1.19 Å2
Refinement stepCycle: LAST / Resolution: 2.5→30.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4866 0 35 164 5065
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0225027
X-RAY DIFFRACTIONr_angle_refined_deg1.4031.9766837
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0135647
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.42921.943211
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.63515726
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7511550
X-RAY DIFFRACTIONr_chiral_restr0.0940.2733
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023914
X-RAY DIFFRACTIONr_nbd_refined0.2170.22064
X-RAY DIFFRACTIONr_nbtor_refined0.3270.43380
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1970.5375
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2280.269
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1910.513
X-RAY DIFFRACTIONr_mcbond_it3.9423286
X-RAY DIFFRACTIONr_mcangle_it5.86135106
X-RAY DIFFRACTIONr_scbond_it4.3921955
X-RAY DIFFRACTIONr_scangle_it6.25431731
LS refinement shellResolution: 2.5→2.562 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.396 127 -
Rwork0.33 2023 -
all-2150 -
obs--99.44 %

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