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- PDB-3nqp: Crystal structure of a SusD superfamily protein (BF1802) from Bac... -

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Basic information

Entry
Database: PDB / ID: 3nqp
TitleCrystal structure of a SusD superfamily protein (BF1802) from Bacteroides fragilis NCTC 9343 at 1.90 A resolution
ComponentsSusD superfamily protein
KeywordsSUGAR BINDING PROTEIN / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


cell outer membrane
Similarity search - Function
Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #390 / SusD-like, N-terminal / Starch-binding associating with outer membrane / RagB/SusD domain / SusD family / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / DI(HYDROXYETHYL)ETHER / Possible outer membrane protein
Similarity search - Component
Biological speciesBacteroides fragilis NCTC 9343 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a SusD superfamily protein (BF1802) from Bacteroides fragilis NCTC 9343 at 1.90 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 29, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software
Revision 1.3Jul 17, 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 1.4Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SusD superfamily protein
B: SusD superfamily protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,00612
Polymers117,3482
Non-polymers65910
Water22,6991260
1
A: SusD superfamily protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1058
Polymers58,6741
Non-polymers4317
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: SusD superfamily protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9014
Polymers58,6741
Non-polymers2273
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)129.093, 87.958, 107.041
Angle α, β, γ (deg.)90.00, 93.38, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2048-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: TYR / Beg label comp-ID: TYR / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 4 / Auth seq-ID: 41 - 538 / Label seq-ID: 17 - 514

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
DetailsANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A MONOMER AS A SIGNIFICANT OLIGOMERIC STATE.

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Components

#1: Protein SusD superfamily protein / Possible outer membrane protein


Mass: 58673.781 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis NCTC 9343 (bacteria)
Strain: ATCC 25285 / NCTC 9343 / Gene: BF1802 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q5LEF0
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1260 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT (26-538) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THE CONSTRUCT (26-538) 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: 2.58 Å3/Da / Density % sol: 52.41 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1290M magnesium acetate, 13.6000% polyethylene glycol 3350, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.97937
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 4, 2009 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979371
ReflectionResolution: 1.9→29.587 Å / Num. all: 93613 / Num. obs: 93613 / % possible obs: 99.5 % / Redundancy: 4 % / Rpim(I) all: 0.087 / Rrim(I) all: 0.173 / Rsym value: 0.15 / Net I/av σ(I): 4.538 / Net I/σ(I): 6.8 / Num. measured all: 371314
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.9-1.953.10.8070.6611.12006765230.4520.8070.6611.794.1
1.95-23.70.6480.5531.42507967010.3320.6480.5532.399.4
2-2.0640.5470.4741.62645965610.2710.5470.4742.8100
2.06-2.1240.4670.4041.92579063840.2320.4670.4043.3100
2.12-2.1940.3970.3442.22502961880.1970.3970.3443.9100
2.19-2.2740.3670.3182.42423659870.1820.3670.3184.2100
2.27-2.364.10.3070.2662.82346757820.1520.3070.2664.8100
2.36-2.454.10.2670.2323.22260155680.1320.2670.2325.4100
2.45-2.564.10.2420.213.52163453280.120.2420.215.8100
2.56-2.694.10.2060.1794.12086151190.1020.2060.1796.7100
2.69-2.834.10.1780.1544.81980548670.0880.1780.1547.7100
2.83-34.10.1470.1285.71885846130.0730.1470.1288.8100
3-3.214.10.1210.1056.81755243150.060.1210.10510.3100
3.21-3.474.10.1040.0917.41643240330.0520.1040.09112.2100
3.47-3.84.10.0990.0867.51517337220.0490.0990.08613.6100
3.8-4.254.10.0840.0738.81365933450.0410.0840.07315.1100
4.25-4.914.10.0790.0689.11222230030.0390.0790.06815.5100
4.91-6.014.10.0890.0778.41026725280.0440.0890.07713.6100
6.01-8.540.0840.0738.8790719650.0420.0840.07313100
8.5-29.5873.90.0680.0589.7421610810.0340.0680.05816.197.6

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0110refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALA3.3.15data scaling
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→29.587 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.94 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 5.149 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.121
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. WATERS WERE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 4. 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 INCORPORAT 5. ACETATE (ACT) IONS, ETHYLENE GLYCOL (EDO), AND PEG-3350 FRAGMENT MOLECULES FROM THE CRYSTALLIZATION/CRYOPROTECTION SOLUTION ARE MODELED. 6. RESIDUES 26-40 AND 168-179 OF CHAIN A AND RESIDUES 26-40 AND 168-178 OF CHAIN B WERE UNMODELED DUE TO DISORDER AND LACK OF ELECTRON DENSITY IN THESE REGIONS. 7. UNEXPLAINED ELECTRON DENSITY NEAR CARBONYL OXYGEN OF THE RESIDUE 525 OF CHAIN A WAS NOT MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.19385 4689 5 %RANDOM
Rwork0.15041 ---
obs0.15259 88913 99.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.438 Å2
Baniso -1Baniso -2Baniso -3
1-1.8 Å20 Å20.07 Å2
2---1.5 Å20 Å2
3----0.29 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.587 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7773 0 43 1260 9076
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0228148
X-RAY DIFFRACTIONr_bond_other_d0.0010.025432
X-RAY DIFFRACTIONr_angle_refined_deg1.4421.9411046
X-RAY DIFFRACTIONr_angle_other_deg0.929313187
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.39351005
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.06124.412408
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.843151346
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.2071542
X-RAY DIFFRACTIONr_chiral_restr0.0890.21173
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.029277
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021755
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.83634919
X-RAY DIFFRACTIONr_mcbond_other0.77832038
X-RAY DIFFRACTIONr_mcangle_it2.72157897
X-RAY DIFFRACTIONr_scbond_it4.42283229
X-RAY DIFFRACTIONr_scangle_it5.801113149
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 6460 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.110.5
medium thermal1.152
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 318 -
Rwork0.264 6193 -
obs--93.82 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.10760.0386-0.06330.2903-0.04420.0991-0.0019-0.0101-0.0005-0.01750.0097-0.01120.00530.0021-0.00780.00850.0008-0.01560.0336-0.00090.036331.809844.728847.634
20.047-0.02480.02240.2592-0.10180.1872-0.0023-0.0036-0.0071-0.01310.0148-0.0047-0.01750.0032-0.01240.0614-0.00760.0220.0094-0.00380.009134.38474.14346.0579
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A41 - 538
2X-RAY DIFFRACTION2B41 - 538

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