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- PDB-3g8r: Crystal structure of putative spore coat polysaccharide biosynthe... -

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Basic information

Entry
Database: PDB / ID: 3g8r
TitleCrystal structure of putative spore coat polysaccharide biosynthesis protein E from Chromobacterium violaceum ATCC 12472
ComponentsProbable spore coat polysaccharide biosynthesis protein E
KeywordsBIOSYNTHETIC PROTEIN / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / NEW YORK STRUCTURAL GENOMIX RESEARCH CONSORTIUM / NYSGXRC / spore coat polysaccharide biosynthesis protein E / PSI-2 / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


carbohydrate biosynthetic process / catalytic activity
Similarity search - Function
N-acetylneuraminic acid synthase, N-terminal / NeuB family / SAF domain / SAF domain / SAF / Type Iii Antifreeze Protein Isoform Hplc 12 / Antifreeze-like/N-acetylneuraminic acid synthase C-terminal domain / Antifreeze-like/N-acetylneuraminic acid synthase C-terminal domain superfamily / Cupin 2, conserved barrel / Cupin domain ...N-acetylneuraminic acid synthase, N-terminal / NeuB family / SAF domain / SAF domain / SAF / Type Iii Antifreeze Protein Isoform Hplc 12 / Antifreeze-like/N-acetylneuraminic acid synthase C-terminal domain / Antifreeze-like/N-acetylneuraminic acid synthase C-terminal domain superfamily / Cupin 2, conserved barrel / Cupin domain / RmlC-like cupin domain superfamily / RmlC-like jelly roll fold / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Probable spore coat polysaccharide biosynthesis protein E
Similarity search - Component
Biological speciesChromobacterium violaceum ATCC 12472 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.49 Å
AuthorsMalashkevich, V.N. / Toro, R. / Morano, C. / 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 spore coat polysaccharide biosynthesis protein E from Chromobacterium violaceum ATCC 12472
Authors: Malashkevich, V.N. / Toro, R. / Morano, C. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionFeb 12, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 1, 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 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 ...audit_author / citation_author / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _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: Probable spore coat polysaccharide biosynthesis protein E
B: Probable spore coat polysaccharide biosynthesis protein E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,5914
Polymers79,4602
Non-polymers1312
Water2,252125
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6440 Å2
ΔGint-34.5 kcal/mol
Surface area28110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.672, 107.672, 164.799
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Refine code: 1 / Auth seq-ID: -999 - 999 / Label seq-ID: -999 - 999

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Probable spore coat polysaccharide biosynthesis protein E


Mass: 39730.230 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chromobacterium violaceum ATCC 12472 (bacteria)
Strain: DSM 30191 / IFO 12614 / JCM 1249 / NCIB 9131 / Gene: CV_3890 / Plasmid: BC-pSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CODON+RIL / References: UniProt: Q7NR94
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 3.01 Å3/Da / Density % sol: 59.07 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2.1 M DL-maleic acid, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 14, 2008
RadiationProtocol: SAD / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.48→50 Å / Num. obs: 57128 / % possible obs: 88 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.143 / Χ2: 1.826 / Net I/σ(I): 13.212
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.48-2.522.40.69911491.103135.6
2.52-2.572.60.8113921.014143.1
2.57-2.622.80.72617041.118151.8
2.62-2.673.10.67420041.135162.3
2.67-2.733.30.7625631.152179.1
2.73-2.793.70.74829611.134190.8
2.79-2.864.30.75931581.154198.2
2.86-2.945.10.64832451.235199.9
2.94-3.035.60.59632561.249199.9
3.03-3.125.90.46132221.2651100
3.12-3.2460.36632611.3221100
3.24-3.375.90.29232381.4751100
3.37-3.525.90.21732411.6481100
3.52-3.75.90.18732831.7981100
3.7-3.945.90.13932412.0911100
3.94-4.245.90.11232232.4551100
4.24-4.675.80.09832752.741100
4.67-5.345.80.09532422.6721100
5.34-6.735.70.08332422.451100
6.73-505.70.05232282.872198.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0070refinement
PDB_EXTRACT3.006data extraction
CBASSdata collection
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.49→20 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.905 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 25.541 / SU ML: 0.255 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.434 / ESU R Free: 0.301 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. U VALUES: RESIDUAL ONLY. 3. The Friedel pairs were used in phasing.
RfactorNum. reflection% reflectionSelection details
Rfree0.278 1575 5 %RANDOM
Rwork0.208 ---
obs0.212 31265 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 105.62 Å2 / Biso mean: 45.023 Å2 / Biso min: 14.21 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20 Å2
2--0.06 Å20 Å2
3----0.13 Å2
Refinement stepCycle: LAST / Resolution: 2.49→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5285 0 2 125 5412
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0225410
X-RAY DIFFRACTIONr_angle_refined_deg1.7691.9517329
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2325673
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.40923.612263
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.56615908
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.371545
X-RAY DIFFRACTIONr_chiral_restr0.1170.2803
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214171
X-RAY DIFFRACTIONr_mcbond_it1.0543.53362
X-RAY DIFFRACTIONr_mcangle_it5.446505409
X-RAY DIFFRACTIONr_scbond_it13.58502048
X-RAY DIFFRACTIONr_scangle_it1.0094.51919
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 2624 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
ATIGHT POSITIONAL0.625
BTIGHT THERMAL4.6210
LS refinement shellResolution: 2.49→2.55 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.474 63 -
Rwork0.331 1041 -
all-1104 -
obs--100 %
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)
10.3780.0207-0.09330.19120.04721.5677-0.04760.0931-0.1327-0.0190.00180.03650.3066-0.02140.04580.0662-0.01020.01790.0245-0.02280.132129.1316-0.9775-19.4476
20.26630.0736-0.11060.20020.08422.15580.00380.02950.0228-0.00730.01740.0203-0.1209-0.0161-0.02120.0073-0.0008-0.00470.00760.0190.067832.676211.5502-3.0195
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 341
2X-RAY DIFFRACTION2B5 - 340

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