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- PDB-4ppy: Crystal structure of a putative acylhydrolase (BF3764) from Bacte... -

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Basic information

Entry
Database: PDB / ID: 4ppy
TitleCrystal structure of a putative acylhydrolase (BF3764) from Bacteroides fragilis NCTC 9343 at 2.00 A resolution
ComponentsPutative acylhydrolase
KeywordsHYDROLASE / PF13472 family / GDSL-like lipase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology: / SGNH hydrolase / SGNH hydrolase-type esterase domain / GDSL-like Lipase/Acylhydrolase family / SGNH hydrolase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Acylhydrolase
Function and homology information
Biological speciesBacteroides fragilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a putative acylhydrolase (BF3764) from Bacteroides fragilis NCTC 9343 at 2.00 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionFeb 27, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 2, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.2Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative acylhydrolase
B: Putative acylhydrolase
C: Putative acylhydrolase


Theoretical massNumber of molelcules
Total (without water)70,5293
Polymers70,5293
Non-polymers00
Water9,062503
1
A: Putative acylhydrolase
B: Putative acylhydrolase


Theoretical massNumber of molelcules
Total (without water)47,0202
Polymers47,0202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-8 kcal/mol
Surface area17810 Å2
MethodPISA
2
C: Putative acylhydrolase

C: Putative acylhydrolase


Theoretical massNumber of molelcules
Total (without water)47,0202
Polymers47,0202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area2020 Å2
ΔGint-7 kcal/mol
Surface area17760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)202.731, 62.213, 61.009
Angle α, β, γ (deg.)90.000, 95.900, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Putative acylhydrolase


Mass: 23509.789 Da / Num. of mol.: 3 / Fragment: UNP residues 27-235
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis (bacteria) / Strain: ATCC 25285 / NCTC 9343 / Gene: BF9343_3663 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): PB1 / References: UniProt: Q5L8Y8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 503 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS CONSTRUCT (RESIDUES 27-235) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THIS CONSTRUCT (RESIDUES 27-235) 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: 2.71 Å3/Da / Density % sol: 54.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.20M magnesium chloride, 30.00% polyethylene glycol 4000, 0.1M tris hydrochloride pH 8.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.979106,0.918401,0.979351
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 17, 2013 / Details: KOHZU: Double Crystal Si(111)
RadiationMonochromator: Double Crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791061
20.9184011
30.9793511
ReflectionResolution: 2→60.686 Å / Num. all: 50307 / Num. obs: 50307 / % possible obs: 98.4 % / Redundancy: 2.1 % / Rsym value: 0.105 / Net I/σ(I): 3.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2-2.052.10.2032.9774436800.20397.9
2.05-2.112.10.1733.4758136020.17398
2.11-2.172.10.1384.4741235130.13898.2
2.17-2.242.10.1493.8714733920.14998.2
2.24-2.312.10.1274.5695533000.12798.3
2.31-2.392.10.1273.8665731930.12798.4
2.39-2.482.10.1254.1647530950.12598.4
2.48-2.582.10.1233.7621029680.12398.5
2.58-2.72.10.1263.9599628680.12698.6
2.7-2.832.10.1124.6568127320.11298.7
2.83-2.982.10.1064.5541926040.10698.3
2.98-3.162.10.1084.1506524580.10898.8
3.16-3.3820.1033.8476823330.10398.6
3.38-3.6520.0834.1436821620.08398.3
3.65-420.1013.3382919590.10198.5
4-4.4720.0636.3372418180.06398.5
4.47-5.1620.0724.6328616310.07299.6
5.16-6.322.10.0714.2286313650.07199.4
6.32-8.942.10.1022.2226110630.10298.6
8.94-60.6862.10.0853.411935710.08595.6

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SOLVEphasing
SCALA3.3.20data scaling
REFMAC5.7.0032refinement
MOSFLMdata reduction
RefinementMethod to determine structure: MAD / Resolution: 2→60.686 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.915 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 6.33 / SU ML: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.174 / ESU R Free: 0.144
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 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 ...Details: 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 SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4.WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5.RAMACHANDRAN OUTLIER AT RESIDUE 112 IN ALL 3 CHAINS IS SUPPORTED BY ELECTRON DENSITY. 6.EXPERIMENTAL PHASES IN THE FORM OF HL COEFFICIENTS WERE USED AS RESTRAINTS DURING CRYSTALLOGRAPHIC REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.2075 2560 5.1 %RANDOM
Rwork0.185 ---
obs0.1861 50307 98 %-
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: 77.83 Å2 / Biso mean: 19.8906 Å2 / Biso min: 7.91 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å20 Å20.67 Å2
2--0.02 Å20 Å2
3----0.35 Å2
Refinement stepCycle: LAST / Resolution: 2→60.686 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4867 0 0 503 5370
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0195091
X-RAY DIFFRACTIONr_bond_other_d0.0040.024803
X-RAY DIFFRACTIONr_angle_refined_deg1.1181.9476951
X-RAY DIFFRACTIONr_angle_other_deg0.945311041
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.135658
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.79825.163246
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.71415803
X-RAY DIFFRACTIONr_dihedral_angle_4_deg4.6591523
X-RAY DIFFRACTIONr_chiral_restr0.0670.2769
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215963
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021210
X-RAY DIFFRACTIONr_mcbond_it0.7271.3972533
X-RAY DIFFRACTIONr_mcbond_other0.7231.3962532
X-RAY DIFFRACTIONr_mcangle_it1.2372.6043170
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 190 -
Rwork0.211 3481 -
all-3671 -
obs--97.66 %
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)
11.46-0.0538-0.22761.60620.19791.53190.0349-0.0349-0.0450.0264-0.002-0.07950.02220.11-0.03290.0450.0058-0.00860.00890.00050.081655.579332.1131.5444
21.74670.003-0.48250.6323-0.32342.0414-0.0639-0.0703-0.05870.11740.02430.10320.116-0.08060.03960.0997-0.00070.010.085-0.00180.08631.414232.723221.4421
31.68780.1776-0.33840.4025-0.14032.00290.0064-0.07310.0850.0130.00620.0387-0.0782-0.0341-0.01250.04010.0098-0.00730.0899-0.00610.09388.998112.45099.5664
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A27 - 235
2X-RAY DIFFRACTION2B28 - 235
3X-RAY DIFFRACTION3C28 - 235

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