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- PDB-2r11: Crystal structure of putative hydrolase (2632844) from Bacillus s... -

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Basic information

Entry
Database: PDB / ID: 2r11
TitleCrystal structure of putative hydrolase (2632844) from Bacillus subtilis at 1.96 A resolution
ComponentsCarboxylesterase NP
KeywordsHYDROLASE / 2632844 / putative hydrolase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / UNKNOWN FUNCTION
Function / homology
Function and homology information


carboxylesterase / carboxylesterase activity
Similarity search - Function
: / Alpha/beta hydrolase family / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / Uncharacterized carboxylesterase nap
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.96 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of putative hydrolase (2632844) from Bacillus subtilis at 1.96 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionAug 21, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: 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 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _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_conn.ptnr2_label_seq_id / _struct_conn_type.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 1.5Oct 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: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
Remark 300 BIOMOLECULE: 1, 2 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY ... BIOMOLECULE: 1, 2 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON BURIED SURFACE AREA. AUTHORS STATE THAT CRYSTAL PACKING ANALYSIS SUPPORTS THE ASSIGNMENT OF A DIMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.
Remark 999 SEQUENCE THE CONSTRUCT CONSISTS OF RESIDUES 1-294 OF THE FULL LENGTH PROTEIN (1-300). IT WAS ... SEQUENCE THE CONSTRUCT CONSISTS OF RESIDUES 1-294 OF THE FULL LENGTH PROTEIN (1-300). IT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHH.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carboxylesterase NP
B: Carboxylesterase NP
C: Carboxylesterase NP
D: Carboxylesterase NP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,6239
Polymers141,2894
Non-polymers3345
Water17,745985
1
A: Carboxylesterase NP
B: Carboxylesterase NP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,7665
Polymers70,6442
Non-polymers1223
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2640 Å2
MethodPISA
2
C: Carboxylesterase NP
D: Carboxylesterase NP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,8574
Polymers70,6442
Non-polymers2122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.590, 97.550, 88.270
Angle α, β, γ (deg.)90.000, 110.010, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: 5 / Auth seq-ID: 13 - 293 / Label seq-ID: 25 - 305

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
DetailsPACKING ANALYSIS SUPPORTS THE ASSIGNMENT OF A DIMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Carboxylesterase NP / Carboxylesterase NA


Mass: 35322.133 Da / Num. of mol.: 4 / Fragment: Residues 1-294
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: 2632844, nap, BSU05440 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: P96688, carboxylesterase

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Non-polymers , 5 types, 990 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 985 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.31 Å3/Da / Density % sol: 46.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9
Details: NANODROP, 14.0% PEG 8000, 0.2M MgCl2, 0.1M CHES pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91837, 0.97934
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 30, 2006 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979341
ReflectionResolution: 1.96→48.795 Å / Num. obs: 85536 / % possible obs: 93 % / Redundancy: 2.9 % / Biso Wilson estimate: 20.86 Å2 / Rmerge(I) obs: 0.094 / Rsym value: 0.094 / Net I/σ(I): 6.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.96-2.072.80.4641.537909133700.46499.8
2.07-2.192.80.2762.535607125340.27699.2
2.19-2.342.80.2452.81918769340.24558.2
2.34-2.532.90.1594.331726110800.15999.8
2.53-2.772.90.1285.329116101600.12899.4
2.77-3.12.90.0937.52647991860.09399.4
3.1-3.582.90.06310.62324380610.06398.9
3.58-4.382.90.0668.21724460310.06687
4.38-6.22.90.037171533652780.03798.3
6.2-48.7952.90.03516.7836829020.03597.2

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
SCALAdata scaling
PDB_EXTRACT2data extraction
MAR345CCDdata collection
XDSdata reduction
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.96→48.795 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.91 / SU B: 4.475 / SU ML: 0.128 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.186 / ESU R Free: 0.174
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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. EDO, MG, CL AND PGE IN THE MODEL ARE PRESENT BASED ON CRYO/CRYSTALLIZATION CONDITIONS. 4. DUE TO PRESENCE OF ICE RINGS, THE DATA FROM THE FOLLOWING RESOLUTION RANGES ARE EXCLUDED: 2.29-2.23, 3.70-3.64. 5. THE ACTIVE SITE TRIAD CONSISTS OF S130-H274-D245.
RfactorNum. reflection% reflectionSelection details
Rfree0.239 4284 5 %RANDOM
Rwork0.181 ---
all0.184 ---
obs0.184 85485 92.9 %-
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 mean: 21.467 Å2
Baniso -1Baniso -2Baniso -3
1-0.73 Å20 Å2-0.22 Å2
2---0.62 Å20 Å2
3----0.25 Å2
Refinement stepCycle: LAST / Resolution: 1.96→48.795 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9225 0 20 985 10230
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0229535
X-RAY DIFFRACTIONr_bond_other_d0.0010.026366
X-RAY DIFFRACTIONr_angle_refined_deg1.3591.94113012
X-RAY DIFFRACTIONr_angle_other_deg0.901315479
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3751180
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.01923.606452
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.82151494
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4361552
X-RAY DIFFRACTIONr_chiral_restr0.0820.21401
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0210695
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022037
X-RAY DIFFRACTIONr_nbd_refined0.2030.22110
X-RAY DIFFRACTIONr_nbd_other0.1930.26684
X-RAY DIFFRACTIONr_nbtor_refined0.1850.24709
X-RAY DIFFRACTIONr_nbtor_other0.0850.24565
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2786
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0270.21
X-RAY DIFFRACTIONr_metal_ion_refined0.0910.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1380.228
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2560.296
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1770.238
X-RAY DIFFRACTIONr_mcbond_it1.62635988
X-RAY DIFFRACTIONr_mcbond_other0.62832303
X-RAY DIFFRACTIONr_mcangle_it2.41959377
X-RAY DIFFRACTIONr_scbond_it4.39384154
X-RAY DIFFRACTIONr_scangle_it5.632113616
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1616MEDIUM POSITIONAL0.190.5
2B1616MEDIUM POSITIONAL0.190.5
3C1616MEDIUM POSITIONAL0.180.5
4D1616MEDIUM POSITIONAL0.190.5
1A1997LOOSE POSITIONAL0.455
2B1997LOOSE POSITIONAL0.375
3C1997LOOSE POSITIONAL0.335
4D1997LOOSE POSITIONAL0.395
1A1616MEDIUM THERMAL1.112
2B1616MEDIUM THERMAL1.122
3C1616MEDIUM THERMAL1.072
4D1616MEDIUM THERMAL1.092
1A1997LOOSE THERMAL2.510
2B1997LOOSE THERMAL2.5810
3C1997LOOSE THERMAL2.4410
4D1997LOOSE THERMAL2.5810
LS refinement shellResolution: 1.96→2.011 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 328 -
Rwork0.243 6423 -
obs-6751 99.57 %

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