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- PDB-1vli: Crystal structure of Spore coat polysaccharide biosynthesis prote... -

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Basic information

Entry
Database: PDB / ID: 1vli
TitleCrystal structure of Spore coat polysaccharide biosynthesis protein spsE (BSU37870) from Bacillus subtilis at 2.38 A resolution
ComponentsSpore coat polysaccharide biosynthesis protein spsE
KeywordsBIOSYNTHETIC PROTEIN / 2636322 / SPORE COAT POLYSACCHARIDE BIOSYNTHESIS PROTEIN SPSE / STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / BSU37870 / SPSE / PSI / Joint Center for Structural Genomics
Function / homology
Function and homology information


N-acylneuraminate-9-phosphate synthase activity / glycosylation / carbohydrate biosynthetic process
Similarity search - Function
N-acetylneuraminic acid synthase, N-terminal / : / NeuB family / SAF domain / SAF / SAF domain / Type Iii Antifreeze Protein Isoform Hplc 12 / Antifreeze-like/N-acetylneuraminic acid synthase C-terminal domain / Antifreeze-like/N-acetylneuraminic acid synthase C-terminal / Antifreeze protein-like domain profile. ...N-acetylneuraminic acid synthase, N-terminal / : / NeuB family / SAF domain / SAF / SAF domain / Type Iii Antifreeze Protein Isoform Hplc 12 / Antifreeze-like/N-acetylneuraminic acid synthase C-terminal domain / Antifreeze-like/N-acetylneuraminic acid synthase C-terminal / Antifreeze protein-like domain profile. / Antifreeze-like/N-acetylneuraminic acid synthase C-terminal domain superfamily / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Spore coat polysaccharide biosynthesis protein SpsE
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.38 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Spore coat polysaccharide biosynthesis protein spsE (BSU37870) from Bacillus subtilis at 2.38 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJul 27, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Spore coat polysaccharide biosynthesis protein spsE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9332
Polymers42,8671
Non-polymers651
Water1,49583
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: Spore coat polysaccharide biosynthesis protein spsE
hetero molecules

A: Spore coat polysaccharide biosynthesis protein spsE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,8654
Polymers85,7342
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+2/31
Buried area2860 Å2
ΔGint-80 kcal/mol
Surface area29220 Å2
MethodPISA
3
A: Spore coat polysaccharide biosynthesis protein spsE
hetero molecules

A: Spore coat polysaccharide biosynthesis protein spsE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,8654
Polymers85,7342
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area1690 Å2
ΔGint-75 kcal/mol
Surface area30390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.578, 70.578, 205.359
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-375-

HOH

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Components

#1: Protein Spore coat polysaccharide biosynthesis protein spsE


Mass: 42867.215 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: spsE, ipa-67d / Production host: Escherichia coli (E. coli) / References: UniProt: P39625
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 1

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Sample preparation

CrystalDensity Matthews: 3.74 Å3/Da / Density % sol: 66.82 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop
Details: 18% PEG MME 2000, 0.04M Tris_base, 0.06M Tris Cl , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
1,21
Diffraction source
SourceSiteBeamlineIDWavelengthWavelength (Å)
SYNCHROTRONSSRL BL9-110.879288
SYNCHROTRONSSRL BL9-120.879288, 0.978780, 0.979359
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 20, 2004 / Details: ADSC Flat mirror
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1single crystal Si(311) bent monochromatorSINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.8792881
20.978781
30.9793591
ReflectionResolution: 2.38→29.29 Å / Num. obs: 24673 / % possible obs: 99.9 % / Redundancy: 6.9 % / Biso Wilson estimate: 61.62 Å2 / Rsym value: 0.076 / Net I/σ(I): 13.5
Reflection shellResolution: 2.38→2.51 Å / Redundancy: 5.9 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 3515 / Rsym value: 0.7 / % possible all: 99.6

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Processing

Software
NameVersionClassification
XDSautodata collection
SCALA4.2)data scaling
SHARPphasing
autoSHARPphasing
SOLOMONphasing
REFMAC5.2.0005refinement
XDSdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.38→29.29 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.941 / SU B: 17.689 / SU ML: 0.192 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.223 / ESU R Free: 0.201
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. A LOW OCCUPIED ZINC WAS TENATIVELY MODELLED TO COORDINATE HIS214 and HIS236 2. THE DENSITY BETWEEN 64-74 APPEARS TO BE CONTINUOUS, HOWEVER, IT IS IMPOSSIBLE TO BUILD ALL THE MISSING ...Details: 1. A LOW OCCUPIED ZINC WAS TENATIVELY MODELLED TO COORDINATE HIS214 and HIS236 2. THE DENSITY BETWEEN 64-74 APPEARS TO BE CONTINUOUS, HOWEVER, IT IS IMPOSSIBLE TO BUILD ALL THE MISSING RESIDUES INTO IT. AS A RESULT, ATOMIC COORDINATES WERE NOT MODELED INTO THIS DENSITY. 3. DIFFICULT TO BUILD LOOPS: 216-220, 244-248. 4. LOOP WITH POOR DENSITY: 293-297. 5. OLIGOMERIC STATE WAS TENATIVELY ASSIGNED AS MONOMER.
RfactorNum. reflection% reflectionSelection details
Rfree0.23799 1256 5.1 %RANDOM
Rwork0.19035 ---
obs0.19271 23362 99.82 %-
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: 62.978 Å2
Baniso -1Baniso -2Baniso -3
1--3.57 Å2-1.78 Å20 Å2
2---3.57 Å20 Å2
3---5.35 Å2
Refinement stepCycle: LAST / Resolution: 2.38→29.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2739 0 1 83 2823
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222800
X-RAY DIFFRACTIONr_angle_refined_deg1.5081.9463803
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4755356
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.70124.667120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.51315458
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1461513
X-RAY DIFFRACTIONr_chiral_restr0.1140.2430
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022127
X-RAY DIFFRACTIONr_nbd_refined0.2080.21181
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.2102
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1190.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1720.26
X-RAY DIFFRACTIONr_mcbond_it2.22531838
X-RAY DIFFRACTIONr_mcangle_it3.71952880
X-RAY DIFFRACTIONr_scbond_it6.43581076
X-RAY DIFFRACTIONr_scangle_it8.73711923
X-RAY DIFFRACTIONr_nbtor_refined0.3080.21924
LS refinement shellResolution: 2.38→2.442 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 92 5.1 %
Rwork0.294 1713 -
obs--99.12 %
Refinement TLS params.Method: refined / Origin x: -0.3153 Å / Origin y: 27.0739 Å / Origin z: 82.8304 Å
111213212223313233
T0.0537 Å20.2215 Å2-0.1619 Å2--0.167 Å2-0.0494 Å2---0.1977 Å2
L1.8562 °2-0.2725 °21.3546 °2-1.4335 °20.2768 °2--2.4594 °2
S-0.149 Å °-0.1278 Å °0.1114 Å °-0.1229 Å °-0.0609 Å °-0.0819 Å °-0.3229 Å °0.0251 Å °0.2099 Å °
Refinement TLS groupSelection: ALL

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