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- PDB-4qhz: Crystal structure of a putative glycosyl hydrolase (BDI_3914) fro... -

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Entry
Database: PDB / ID: 4qhz
TitleCrystal structure of a putative glycosyl hydrolase (BDI_3914) from Parabacteroides distasonis ATCC 8503 at 2.13 A resolution
Componentsputative glycosyl hydrolase
KeywordsHYDROLASE / PF06439 family protein / DUF1080 / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology3-keto-disaccharide hydrolase / 3-keto-disaccharide hydrolase / Exo-inulinase; domain 1 / Jelly Rolls / Sandwich / Mainly Beta / metal ion binding / DUF1080 domain-containing protein
Function and homology information
Biological speciesParabacteroides distasonis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.13 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a putative glycosyl hydrolase (BDI_3914) from Parabacteroides distasonis ATCC 8503 at 2.13 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMay 30, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 30, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Feb 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.pdbx_leaving_atom_flag / _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_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: putative glycosyl hydrolase
B: putative glycosyl hydrolase
C: putative glycosyl hydrolase
D: putative glycosyl hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,03011
Polymers111,7474
Non-polymers2837
Water16,394910
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14820 Å2
ΔGint-120 kcal/mol
Surface area37760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.774, 144.763, 82.452
Angle α, β, γ (deg.)90.000, 101.270, 90.000
Int Tables number4
Space group name H-MP1211
DetailsCRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A TETRAMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein
putative glycosyl hydrolase


Mass: 27936.746 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Parabacteroides distasonis (bacteria) / Strain: ATCC 8503 / Gene: BDI_3914 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: A6LIT1
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 910 / Source method: isolated from a natural source / Formula: H2O
Sequence details1.THIS CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...1.THIS CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 21-265 OF THE TARGET SEQUENCE. 2. THE PROTEIN WAS REDUCTIVELY METHYLATED PRIOR TO CRYSTALLIZATION. ALL LYSINE RESIDUES (EXCEPT RESIDUES 102, 169, AND 197) HAVE BEEN MODELED AS MLY.

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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: 2.5 Å3/Da / Density % sol: 50.84 %
Description: THE STRUCTURE WAS SOLVED BY THREE WAVELENGTH MAD METHOD AT 2.40A RESOLUTION. THE STRUCTURE WAS REFINED AT 2.13A RESOLUTION AGAINST A DATASET COLLECTED FROM A DIFFERENT CRYSTAL.
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop
Details: 0.2M magnesium acetate, 20.0% polyethylene glycol 3350, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL11-110.97895
SYNCHROTRONSSRL BL9-220.91837,0.97941
Detector
TypeIDDetectorDateDetails
DECTRIS PILATUS 6M1PIXELNov 27, 2013Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)
MARMOSAIC 325 mm CCD2CCDFeb 13, 2014double crystal monochromator
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1single crystal Si(111) bentMADMx-ray1
2double crystalMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.978951
20.918371
30.979411
ReflectionResolution: 2.13→48.254 Å / Num. obs: 58318 / % possible obs: 95 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 26.92 Å2 / Rmerge(I) obs: 0.111 / Net I/σ(I): 6.96
Reflection shell

Diffraction-ID: 1,2

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.13-2.210.4772.114623615996.6
2.21-2.290.4322.412372527894.2
2.29-2.40.3552.914412613095.4
2.4-2.520.2743.613800567997.2
2.52-2.680.2294.214279596096
2.68-2.890.1685.513526574392.7
2.89-3.180.1197.714551594396.7
3.18-3.640.07211.413932576994.2
3.64-4.570.05314.714198577594.8
4.570.05615.114117582092.4

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SOLVEphasing
REFMAC5.7.0032refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.13→48.254 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.939 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 8.623 / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.237 / ESU R Free: 0.176
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 INCORPORATION. 5. THE PROTEIN WAS REDUCTIVELY METHYLATED PRIOR RO CRYSTALLIZATION. THEREFORE ALL LYSINE RESIDUES (EXCEPT RESIDUES 102, 169, AND 197) HAVE BEEN MODELED AS MLY. ELECTRON DENSITY SUGGESTS THAT THESE THREE RESIDUES ARE UNMODIFIED. 6. MAGNESIUM (MG) IONS AND 1,2-ETHANEDIOL (EDO) MOLECULES FROM THE CRYSTALLIZATION/CRYOPROTECTION SOLUTION ARE MODELED. 7. THE REFINEMENT WAS RESTRAINED AGAINST THE MAD PHASES FROM A CRYSTAL THAT WAS USED TO OBTAIN THE STRUCTURE SOLUTION.
RfactorNum. reflection% reflectionSelection details
Rfree0.2035 2948 5.1 %RANDOM
Rwork0.1707 ---
obs0.1724 55339 95.03 %-
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 max: 91.75 Å2 / Biso mean: 27.0401 Å2 / Biso min: 11.39 Å2
Baniso -1Baniso -2Baniso -3
1-1.21 Å20 Å20.74 Å2
2---0.3 Å2-0 Å2
3----0.99 Å2
Refinement stepCycle: LAST / Resolution: 2.13→48.254 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7530 0 16 910 8456
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0197796
X-RAY DIFFRACTIONr_bond_other_d0.0030.027199
X-RAY DIFFRACTIONr_angle_refined_deg1.1991.97410641
X-RAY DIFFRACTIONr_angle_other_deg0.775316605
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.985962
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.61425.211355
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.45915986
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.5031520
X-RAY DIFFRACTIONr_chiral_restr0.0410.21164
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0218884
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021784
X-RAY DIFFRACTIONr_mcbond_it1.3783.6913821
X-RAY DIFFRACTIONr_mcbond_other1.3783.693820
X-RAY DIFFRACTIONr_mcangle_it2.0456.9074774
LS refinement shellResolution: 2.13→2.185 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 206 -
Rwork0.229 4190 -
all-4396 -
obs--97 %
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)
10.3351-0.0303-0.12820.785-0.12140.6433-0.0134-0.0036-0.0205-0.01710.00390.0570.0348-0.07130.00950.0057-0.0041-0.0070.0456-0.00710.021-8.29378.92729.993
20.5250.15040.03570.74920.07480.5793-0.0006-0.02410.0835-0.01750.0113-0.097-0.02970.0571-0.01070.004-0.0019-0.00070.0289-0.00250.0438.68795.21930.368
30.1760.0298-0.06020.79450.2610.5277-0.00030.01510.0078-0.06690.0014-0.05990.05330.0649-0.00110.06790.0267-0.00590.03380.00440.02645.92579.124-6.418
40.3031-0.0193-0.06011.04830.02330.51230.03420.02120.0568-0.1275-0.02640.1019-0.0837-0.0864-0.00790.08310.0393-0.01750.04670.00010.0527-5.95196.747-5.902
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A30 - 265
2X-RAY DIFFRACTION2B30 - 265
3X-RAY DIFFRACTION3C26 - 265
4X-RAY DIFFRACTION4D26 - 265

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