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Basic information

Entry
Database: PDB / ID: 3imm
TitleCrystal structure of Putative glycosyl hydrolase (YP_001301887.1) from Parabacteroides distasonis ATCC 8503 at 2.00 A resolution
ComponentsPutative secreted glycosylhydrolase
KeywordsHYDROLASE / YP_001301887.1 / Putative glycosyl hydrolase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology3-keto-disaccharide hydrolase / 3-keto-alpha-glucoside-1,2-lyase-like domain / Exo-inulinase; domain 1 / hydrolase activity / Jelly Rolls / Sandwich / Mainly Beta / Putative secreted glycosylhydrolase
Function and homology information
Biological speciesParabacteroides distasonis ATCC 8503 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Putative glycosyl hydrolase (YP_001301887.1) from Parabacteroides distasonis ATCC 8503 at 2.00 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionAug 10, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / 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 / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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 1.5Nov 20, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id ..._pdbx_entry_details.has_protein_modification / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative secreted glycosylhydrolase
B: Putative secreted glycosylhydrolase
C: Putative secreted glycosylhydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,7238
Polymers68,4963
Non-polymers2275
Water7,116395
1
A: Putative secreted glycosylhydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8552
Polymers22,8321
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative secreted glycosylhydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8913
Polymers22,8321
Non-polymers582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Putative secreted glycosylhydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9773
Polymers22,8321
Non-polymers1452
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.404, 45.404, 241.069
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
12A
22B
32C

NCS domain segments:

Component-ID: 1 / Refine code: 4

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNGLUGLUAA26 - 1115 - 90
21ASNASNGLUGLUBB26 - 1115 - 90
31ASNASNGLUGLUCC26 - 1115 - 90
12GLYGLYLEULEUAA116 - 22295 - 201
22GLYGLYLEULEUBB116 - 22295 - 201
32GLYGLYLEULEUCC116 - 22295 - 201

NCS ensembles :
ID
1
2
DetailsANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

#1: Protein Putative secreted glycosylhydrolase


Mass: 22832.152 Da / Num. of mol.: 3 / Fragment: sequence database residues 23-222
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Parabacteroides distasonis ATCC 8503 (bacteria)
Gene: BDI_0489, YP_001301887.1 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: A6L9A1
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 395 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT (RESIDUES 23-222) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THE CONSTRUCT (RESIDUES 23-222) 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: 2.09 Å3/Da / Density % sol: 41.27 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2000M NaCl, 30.0000% PEG-3000, 0.1M TRIS pH 7.0, 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: 0.91162,0.97805,0.97874
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 15, 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
10.911621
20.978051
30.978741
ReflectionResolution: 2→28.105 Å / Num. obs: 37531 / % possible obs: 99.7 % / Redundancy: 2.9 % / Biso Wilson estimate: 26.958 Å2 / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 9.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2-2.052.50.3682.2690627090.36896.9
2.05-2.112.90.2663.2771026810.266100
2.11-2.172.90.223.9769026710.22100
2.17-2.242.90.1964.4721825210.196100
2.24-2.312.90.1834.9722424980.183100
2.31-2.392.90.1655.7714324670.165100
2.39-2.482.90.1346.8647122540.134100
2.48-2.582.90.1187.9636721970.118100
2.58-2.72.90.1078.8635021930.107100
2.7-2.832.90.09710.6593220490.097100
2.83-2.982.90.08412.2553219040.084100
2.98-3.162.90.07513.9542918530.075100
3.16-3.382.90.06815.5497417130.068100
3.38-3.652.90.06617.4468916080.066100
3.65-42.90.06218.9435214980.062100
4-4.472.90.05819.6390213440.058100
4.47-5.162.90.05319.7344411750.053100
5.16-6.322.90.05619.8294710100.056100
6.32-8.942.90.06220.722247730.062100
8.94-28.12.80.05722.111654130.05796.5

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SOLVEphasing
MolProbity3beta29model building
SCALA3.2.5data scaling
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MAD / Resolution: 2→28.105 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.942 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 9.119 / SU ML: 0.135 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.197 / ESU R Free: 0.173
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS OTHER REFINEMENT REMARKS: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS OTHER REFINEMENT REMARKS: 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. SODIUM (NA) AND CHLORIDE (CL) IONS AND 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL (TRS) FROM THE CRYSTALLIZATION SOLUTION WERE MODELED INTO THE STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.222 1876 5 %RANDOM
Rwork0.163 ---
obs0.166 37453 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 61.09 Å2 / Biso mean: 31.58 Å2 / Biso min: 15.81 Å2
Baniso -1Baniso -2Baniso -3
1-1.59 Å20.79 Å20 Å2
2--1.59 Å20 Å2
3----2.38 Å2
Refinement stepCycle: LAST / Resolution: 2→28.105 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4669 0 12 395 5076
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224944
X-RAY DIFFRACTIONr_bond_other_d0.0010.023334
X-RAY DIFFRACTIONr_angle_refined_deg1.5291.9336726
X-RAY DIFFRACTIONr_angle_other_deg0.91838191
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0515616
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.09425.721222
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.29215845
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.677159
X-RAY DIFFRACTIONr_chiral_restr0.0980.2693
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025565
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02944
X-RAY DIFFRACTIONr_nbd_refined0.2140.2842
X-RAY DIFFRACTIONr_nbd_other0.1930.23434
X-RAY DIFFRACTIONr_nbtor_refined0.1790.22314
X-RAY DIFFRACTIONr_nbtor_other0.0880.22509
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2357
X-RAY DIFFRACTIONr_metal_ion_refined0.1170.27
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1890.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2770.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1330.222
X-RAY DIFFRACTIONr_mcbond_it1.49233018
X-RAY DIFFRACTIONr_mcbond_other0.68831238
X-RAY DIFFRACTIONr_mcangle_it2.20444885
X-RAY DIFFRACTIONr_scbond_it2.76952064
X-RAY DIFFRACTIONr_scangle_it3.68161841
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1052MEDIUM POSITIONAL0.490.5
12B1052MEDIUM POSITIONAL0.490.5
13C1052MEDIUM POSITIONAL0.460.5
11A1052MEDIUM THERMAL1.112
12B1052MEDIUM THERMAL1.132
13C1052MEDIUM THERMAL1.112
21A1384MEDIUM POSITIONAL0.570.5
22B1384MEDIUM POSITIONAL0.490.5
23C1384MEDIUM POSITIONAL0.520.5
21A1384MEDIUM THERMAL1.192
22B1384MEDIUM THERMAL1.112
23C1384MEDIUM THERMAL1.212
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 133 -
Rwork0.21 2572 -
all-2705 -
obs--96.92 %
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)
10.7919-0.01010.01871.05560.01051.66480.05250.0509-0.0597-0.1907-0.05640.08880.2323-0.07160.00380.040.03010.0028-0.18050.0066-0.093718.7256-22.2911-2.6889
236.4451-4.33665.94637.6032-13.094822.6209-0.00061.0588-0.73890.9547-0.85132.14122.74631.04920.85190.4216-0.05530.08860.0761-0.00450.083830.539-1.5552-9.3188
32.9456-0.84531.60174.0478-0.88862.38380.02650.03690.1089-0.0967-0.0636-0.0924-0.44970.01330.03710.05460.04390.0471-0.18670.0226-0.094320.6805-3.366-1.1327
40.783-0.26280.04541.4824-0.07591.51890.04270.00610.0116-0.0876-0.02750.1016-0.0597-0.1606-0.0152-0.0130.04440.0166-0.16030.0089-0.100616.2308-11.87050.2079
50.7267-0.39680.43351.8795-1.38882.44420.070.02410.09340.1136-0.0592-0.0242-0.43620.01-0.01070.04080.01240.0284-0.16470.014-0.097511.6848.633521.2
6104.418442.86996.307296.0824-39.9711100.9783-1.3683-3.1639-3.95580.1269-2.9894-1.60662.67480.04784.35770.42140.0476-0.00360.511-0.01590.5418-0.0271-9.69715.4795
73.4661-0.2949-0.26483.0016-1.89292.10770.03730.033-0.2343-0.21820.10190.37050.2306-0.2272-0.1392-0.0383-0.0144-0.0341-0.12360.0282-0.05295.1096-8.844625.1597
80.7852-0.25640.44411.8063-1.07062.17350.0667-0.08240.00060.07550.01530.0934-0.1801-0.0704-0.082-0.05310.00680.0248-0.14770.0144-0.103610.3203-0.713127.1287
91.185-0.57390.87031.2033-0.79283.62940.1802-0.1063-0.173-0.24840.03430.16430.4686-0.222-0.21450.061-0.1902-0.0646-0.01680.0495-0.078610.3593-20.553849.0118
1089.18838.5901-33.071578.8365-51.260888.81562.7335-1.4580.67331.8468-3.99171.2960.47421.46441.25820.47670.05930.08840.44280.15930.359728.3765-9.194643.8689
112.691-3.09331.55614.4155-0.40063.14140.0897-0.01060.3314-0.0435-0.2471-0.4158-0.19670.3110.15740.0385-0.2011-0.01220.02270.0775-0.057922.8631-6.784552.9045
121.1398-0.38830.66091.7155-1.00052.83890.092-0.1982-0.03120.0421-0.0387-0.0231-0.0933-0.0919-0.05330.0034-0.1679-0.02120.02270.0215-0.14114.8275-12.202354.8748
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A26 - 110
2X-RAY DIFFRACTION2A111 - 115
3X-RAY DIFFRACTION3A116 - 135
4X-RAY DIFFRACTION4A136 - 222
5X-RAY DIFFRACTION5B26 - 110
6X-RAY DIFFRACTION6B111 - 115
7X-RAY DIFFRACTION7B116 - 135
8X-RAY DIFFRACTION8B136 - 222
9X-RAY DIFFRACTION9C26 - 110
10X-RAY DIFFRACTION10C111 - 115
11X-RAY DIFFRACTION11C116 - 135
12X-RAY DIFFRACTION12C136 - 222

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