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- PDB-2hx5: Crystal structure of a putative thioesterase (pmt_2055) from proc... -

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Basic information

Entry
Database: PDB / ID: 2hx5
TitleCrystal structure of a putative thioesterase (pmt_2055) from prochlorococcus marinus str. mit 9313 at 1.50 A resolution
ComponentsHypothetical protein
KeywordsHYDROLASE / Thioesterase/thiol ester dehydrase-isomerase fold / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


1,4-dihydroxy-2-naphthoyl-CoA hydrolase / phylloquinone biosynthetic process / 1,4-dihydroxy-2-naphthoyl-CoA thioesterase activity
Similarity search - Function
1,4-dihydroxy-2-naphthoyl-CoA hydrolase / Thioesterase-like superfamily / : / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
2-ETHOXYETHANOL / 1,4-dihydroxy-2-naphthoyl-CoA hydrolase
Similarity search - Component
Biological speciesProchlorococcus marinus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be Published
Title: Crystal structure of hypothetical protein (NP_895880.1) from Prochlorococcus marinus MIT9313 at 1.50 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionAug 2, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Jan 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 1.6Nov 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 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY DATA SUPPORTS THE ASSIGNMENT OF A TETRAMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7073
Polymers17,5261
Non-polymers1802
Water2,558142
1
A: Hypothetical protein
hetero molecules

A: Hypothetical protein
hetero molecules

A: Hypothetical protein
hetero molecules

A: Hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,82712
Polymers70,1064
Non-polymers7218
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_565x,-y+1,-z1
Unit cell
Length a, b, c (Å)104.220, 104.220, 104.220
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23
DetailsSIZE EXCLUSION CHROMATOGRAPHY DATA SUPPORTS THE ASSIGNMENT OF A TETRAMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE

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Components

#1: Protein Hypothetical protein


Mass: 17526.422 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Prochlorococcus marinus (bacteria) / Strain: MIT 9313 / Gene: NP_895880.1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7V4A7
#2: Chemical ChemComp-ETX / 2-ETHOXYETHANOL


Mass: 90.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.19 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 6.5
Details: 35.0% 2-ethoxyethanol, 0.1M Cacodylate pH 6.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 17, 2006 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.5→27.853 Å / Num. obs: 30132 / % possible obs: 95.3 % / Biso Wilson estimate: 25.327 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 11.55
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique all% possible all
1.5-1.550.741.916454457182.8
1.55-1.620.6092.422469598490.4
1.62-1.690.4763.119316512592.4
1.69-1.780.3514.121019557094.6
1.78-1.890.2425.821209559796.5
1.89-2.040.1869.430688583798.1
2.04-2.240.13814.237955567999.2
2.24-2.560.10117.538662576399.4
2.560.0722.539731591999.8

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
SHELXphasing
REFMAC5.2.0019refinement
XSCALEdata scaling
PDB_EXTRACT2data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.5→27.853 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.965 / SU B: 2.317 / SU ML: 0.042 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.058 / ESU R Free: 0.061
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 ...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) THERE IS UNKNOWN DENSITY NEAR GLU104. THIS WAS LEFT UNMODELED. THE UNKNOWN DENSITY IS LOCATED NEAR THE ACTIVE SITE OF THE PROTEIN. THIS COULD BE PART OF COA. (4). ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.182 1524 5.1 %RANDOM
Rwork0.155 ---
all0.157 ---
obs-30131 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.349 Å2
Refinement stepCycle: LAST / Resolution: 1.5→27.853 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1169 0 12 142 1323
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0211278
X-RAY DIFFRACTIONr_bond_other_d0.0110.02898
X-RAY DIFFRACTIONr_angle_refined_deg1.7281.9311740
X-RAY DIFFRACTIONr_angle_other_deg1.37932152
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9345157
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.01822.35368
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.88615203
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.0871515
X-RAY DIFFRACTIONr_chiral_restr0.1620.2179
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021472
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02295
X-RAY DIFFRACTIONr_nbd_refined0.2270.2225
X-RAY DIFFRACTIONr_nbd_other0.210.2917
X-RAY DIFFRACTIONr_nbtor_refined0.1790.2605
X-RAY DIFFRACTIONr_nbtor_other0.0890.2673
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.294
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1820.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3140.256
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1460.222
X-RAY DIFFRACTIONr_mcbond_it2.6353915
X-RAY DIFFRACTIONr_mcbond_other0.4843299
X-RAY DIFFRACTIONr_mcangle_it2.95751240
X-RAY DIFFRACTIONr_scbond_it4.9628565
X-RAY DIFFRACTIONr_scangle_it7.2611500
LS refinement shellResolution: 1.501→1.54 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 110 -
Rwork0.237 2046 -
obs-2156 97.42 %
Refinement TLS params.Method: refined / Origin x: 40.3951 Å / Origin y: 46.5673 Å / Origin z: 11.0461 Å
111213212223313233
T-0.0305 Å20.0078 Å20.0254 Å2--0.0352 Å20.0109 Å2---0.0196 Å2
L0.6636 °2-0.0713 °20.0037 °2-1.0044 °20.1947 °2--0.6211 °2
S0.0048 Å °-0.1046 Å °-0.0117 Å °0.1618 Å °-0.0144 Å °0.1252 Å °0.0422 Å °0.0178 Å °0.0096 Å °
Refinement TLS groupSelection: ALL

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