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- PDB-3b5e: Crystal structure of carboxylesterase (NP_108484.1) from Mesorhiz... -

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Basic information

Entry
Database: PDB / ID: 3b5e
TitleCrystal structure of carboxylesterase (NP_108484.1) from Mesorhizobium loti at 1.75 A resolution
ComponentsMll8374 protein
KeywordsHYDROLASE / NP_108484.1 / Carboxylesterase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homologyAlpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Mll8374 protein
Function and homology information
Biological speciesMesorhizobium loti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.75 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of carboxylesterase (NP_108484.1) from Mesorhizobium loti at 1.75 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionOct 25, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: 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 1.4Jan 25, 2023Group: Database references / Derived calculations / Category: database_2 / 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_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 16, 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 / _struct_ncs_dom_lim.end_auth_comp_id
Remark 999 SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ... SEQUENCE THE CONSTRUCT 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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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mll8374 protein
B: Mll8374 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,45425
Polymers47,9582
Non-polymers1,49623
Water8,683482
1
A: Mll8374 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,75813
Polymers23,9791
Non-polymers77912
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Mll8374 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,69612
Polymers23,9791
Non-polymers71711
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.160, 105.000, 123.620
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: 4 / Auth seq-ID: 7 - 215 / Label seq-ID: 8 - 216

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
DetailsSIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION BUT CRYSTAL PACKING ANALYSIS DOES NOT REVEAL ANY INTERFACES THAT ARE LIKELY STABLE AS A DIMER.

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Components

#1: Protein Mll8374 protein


Mass: 23978.990 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mesorhizobium loti (bacteria) / Strain: MAFF303099 / Gene: NP_108484.1, mll8374 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q983D6
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 482 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsREMARK 999 REMARK 999 SEQUENCE: THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION REMARK 999 TAG ...REMARK 999 REMARK 999 SEQUENCE: THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION REMARK 999 TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE REMARK 999 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: 3.19 Å3/Da / Density % sol: 61.45 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 10.5
Details: NANODROP, 2.0M (NH4)2SO4, 0.2M Li2SO4, 0.1M CAPS pH 10.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.0000, 0.9795
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 15, 2007
RadiationMonochromator: Double Crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97951
ReflectionResolution: 1.75→29.643 Å / Num. obs: 62118 / % possible obs: 97.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 28.45 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 10.85
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.75-1.810.5561.41097910112187.8
1.81-1.890.4631.81905213076199.4
1.89-1.970.3312.51650410989199.4
1.97-2.070.2213.61738211491199.4
2.07-2.20.1485.31826411994199.3
2.2-2.370.1017.61817411993199.3
2.37-2.610.0710.71835812023199.2
2.61-2.990.045161825711900198.6
2.99-3.760.02625.81793211643197.7
3.76-29.6430.01933.51871811540195.4

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3data extraction
ADSCQuantumdata collection
XDSdata reduction
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.75→29.643 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.957 / SU B: 4.214 / SU ML: 0.068 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.089 / ESU R Free: 0.088
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. 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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. SO4 AND ETHYLENE GLYCOL ARE MODELED BASED ON CRYSTALLIZATION AND CRYO CONDITIONS. 5. UNEXPLAINED ELECTRON DENSITIES NEAR RESIDUES 108 AND 209 IN SUBUNIT A WERE NOT MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.19 3150 5.1 %RANDOM
Rwork0.163 ---
obs0.165 62069 98.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.283 Å2
Baniso -1Baniso -2Baniso -3
1-0.51 Å20 Å20 Å2
2--0.16 Å20 Å2
3----0.67 Å2
Refinement stepCycle: LAST / Resolution: 1.75→29.643 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3173 0 94 482 3749
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0213540
X-RAY DIFFRACTIONr_bond_other_d0.0010.022419
X-RAY DIFFRACTIONr_angle_refined_deg1.5261.9844823
X-RAY DIFFRACTIONr_angle_other_deg1.03135875
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0115466
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.33422.5144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.26615527
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6241533
X-RAY DIFFRACTIONr_chiral_restr0.0850.2550
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024031
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02730
X-RAY DIFFRACTIONr_nbd_refined0.2010.2675
X-RAY DIFFRACTIONr_nbd_other0.2020.22599
X-RAY DIFFRACTIONr_nbtor_refined0.1680.21670
X-RAY DIFFRACTIONr_nbtor_other0.0840.21872
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2343
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0830.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1710.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1120.228
X-RAY DIFFRACTIONr_mcbond_it1.91432438
X-RAY DIFFRACTIONr_mcbond_other0.5593895
X-RAY DIFFRACTIONr_mcangle_it2.62953633
X-RAY DIFFRACTIONr_scbond_it4.49681364
X-RAY DIFFRACTIONr_scangle_it6.715111189
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2696 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
MEDIUM POSITIONAL0.330.5
MEDIUM THERMAL0.782
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 224 -
Rwork0.301 4002 -
all-4226 -
obs--93 %
Refinement TLS params.

S11: 0.0289 Å ° / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)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)
10.67170.19430.20920.73910.51631.2835-0.0640.07910.1472-0.0566-0.0194-0.0365-0.0580.0277-0.0068-0.0222-0.013-0.0339-0.0232-0.016145.587542.424324.6654
20.6411-0.02210.04870.5458-0.12441.3922-0.051-0.07570.08130.0009-0.02070.1145-0.0428-0.0298-0.0741-0.0081-0.0121-0.05530.0131-0.02525.409213.620212.2196
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA7 - 2158 - 216
2X-RAY DIFFRACTION2BB3 - 2154 - 216

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