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- PDB-2hbo: Crystal structure of a thioesterase superfamily protein (cc_3309)... -

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Basic information

Entry
Database: PDB / ID: 2hbo
TitleCrystal structure of a thioesterase superfamily protein (cc_3309) from caulobacter vibrioides at 1.85 A resolution
ComponentsHypothetical protein (np_422103.1)
KeywordsHYDROLASE / Thioesterase/thiol ester dehydrase-isomerase fold / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homologythiolester hydrolase activity / Thioesterase domain / Thioesterase superfamily / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta / Thioesterase domain-containing protein
Function and homology information
Biological speciesCaulobacter vibrioides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.85 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of hypothetical protein (np_422103.1) from Caulobacter crescentus at 1.85 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 14, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _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 / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE 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

Downloads & links

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Assembly

Deposited unit
A: Hypothetical protein (np_422103.1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2594
Polymers17,7801
Non-polymers4793
Water1,15364
1
A: Hypothetical protein (np_422103.1)
hetero molecules

A: Hypothetical protein (np_422103.1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5178
Polymers35,5602
Non-polymers9576
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Unit cell
Length a, b, c (Å)53.440, 53.440, 99.090
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein Hypothetical protein (np_422103.1)


Mass: 17780.152 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caulobacter vibrioides (bacteria) / Gene: np_422103.1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9A395
#2: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000


Mass: 354.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)Description
12.141.08DATA FROM A SE-MET CONTAINING CRYSTAL IN SPACEGROUP P4(3)2(1)2 WAS USED FOR THE MAD PHASING EXPERIMENTS AT 2.1 ANGSTROMS RESOLUTION. THIS MAD STRUCTURE WAS USE D AS A MOLECULAR REPLACEMENT MODEL TO PHASE THIS STRUCTURE AT 1.85 ANGSTROMS RES OLUTION IN THE P4(2)2(1)2 SPACEGROUP.
2DATA FROM A SE-MET CONTAINING CRYSTAL IN SPACEGROUP P4(3)2(1)2 WAS USED FOR THE MAD PHASING EXPERIMENTS AT 2.1 ANGSTROMS RESOLUTION. THIS MAD STRUCTURE WAS USE D AS A MOLECULAR REPLACEMENT MODEL TO PHASE THIS STRUCTURE AT 1.85 ANGSTROMS RES OLUTION IN THE P4(2)2(1)2 SPACEGROUP.
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2771vapor diffusion, sitting drop, nanodrop6.60.2M NH4Formate, 20.0% PEG-3350, No Buffer, pH 6.6, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K
2772vapor diffusion, sitting drop, nanodrop4.240.0% PEG-300, 0.1M Phosphate Citrate, pH 4.2, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineIDWavelengthWavelength (Å)
SYNCHROTRONSSRL BL9-210.91162
SYNCHROTRONSSRL BL11-120.979008, 0.979318, 0.918370
Detector
TypeIDDetectorDateDetails
MARMOSAIC 325 mm CCD1CCDMay 14, 2006Flat collimating mirror, toroid focusing mirror
ADSC QUANTUM 3152CCDMay 8, 2006Flat mirror (vertical focusing)
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-IDMonochromator
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray2Single crystal Si(111) bent monochromator (horizontal focusing)
Radiation wavelength
IDWavelength (Å)Relative weight
10.911621
20.9790081
30.9793181
40.918371
ReflectionResolution: 1.85→50 Å / Num. obs: 12896 / % possible obs: 99.8 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.073 / Χ2: 0.973 / Net I/σ(I): 13.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.85-1.95.50.8058870.9741,2100
1.9-1.956.90.69001.0371,2100
1.95-27.10.4958841.0081,2100
2-2.077.10.3979120.9961,2100
2.07-2.147.10.3179040.9191,2100
2.14-2.237.10.2238990.9541,2100
2.23-2.337.10.1989010.9611,2100
2.33-2.457.10.1619091.0771,2100
2.45-2.617.10.1269180.9781,2100
2.61-2.817.10.0969220.9641,2100
2.81-3.0970.079200.9231,2100
3.09-3.546.90.0549501.0621,299.9
3.54-4.466.60.0439570.8631,299.5
4.46-5060.05210330.8961,298.7

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
REFMAC5.2.0005refinement
SCALEPACKdata scaling
PDB_EXTRACT2data extraction
RefinementMethod to determine structure: MAD / Resolution: 1.85→28.1 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.946 / SU B: 8.068 / SU ML: 0.117 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.158 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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. PEG-3350 HAS BEEN PARTIALLED MODELED AS PE4. 4. THERE ARE SOME POSITIVE DIFFERENCE DENSITIES AROUND PEG THAT SUGGEST THAT PEG MOLECULE MIGHT OCCUPY ALTERNATE CONFORMATIONS WITH PARTIAL OCCUPANCIES. 5. ETHYLENE GLYCOL (EDO) FROM CRYO CONDITION HAS BEEN MODELED. 6. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.244 628 4.9 %RANDOM
Rwork0.208 ---
obs0.21 12846 99.76 %-
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: 36.857 Å2
Baniso -1Baniso -2Baniso -3
1--1.75 Å20 Å20 Å2
2---1.75 Å20 Å2
3---3.51 Å2
Refinement stepCycle: LAST / Resolution: 1.85→28.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1089 0 31 64 1184
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221165
X-RAY DIFFRACTIONr_bond_other_d0.0020.021094
X-RAY DIFFRACTIONr_angle_refined_deg1.561.9521562
X-RAY DIFFRACTIONr_angle_other_deg0.82332516
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9015147
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.0921.63349
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.46515187
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8171511
X-RAY DIFFRACTIONr_chiral_restr0.0840.2159
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021290
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02264
X-RAY DIFFRACTIONr_nbd_refined0.2230.2212
X-RAY DIFFRACTIONr_nbd_other0.2030.21169
X-RAY DIFFRACTIONr_nbtor_refined0.180.2555
X-RAY DIFFRACTIONr_nbtor_other0.0850.2716
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.256
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1260.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1920.275
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1280.216
X-RAY DIFFRACTIONr_mcbond_it1.5982752
X-RAY DIFFRACTIONr_mcbond_other0.2972304
X-RAY DIFFRACTIONr_mcangle_it2.33841115
X-RAY DIFFRACTIONr_scbond_it3.3824519
X-RAY DIFFRACTIONr_scangle_it4.126444
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 38 -
Rwork0.298 867 -
obs-905 98.37 %
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)
111.695812.00656.043822.72-4.582214.3167-0.1885-0.1391-0.39981.7376-0.5626-0.73130.6692-0.76150.7510.21150.0340.06650.0282-0.0253-0.03857.755-20.492-7.389
21.08850.6675-0.30412.4107-0.25790.65430.00150.10290.05690.1027-0.05210.0175-0.0319-0.06560.0506-0.0716-0.02560.03350.0546-0.037-0.21387.773-7.513-16.776
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDAuth seq-IDLabel seq-ID
1112 - 1713 - 18
2218 - 15319 - 154

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