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- PDB-6v77: Crystal structure of a putative HpcE protein from Mycobacterium s... -

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Basic information

Entry
Database: PDB / ID: 6v77
TitleCrystal structure of a putative HpcE protein from Mycobacterium smegmatis
ComponentsPutative HpcE protein
KeywordsUNKNOWN FUNCTION / SSGCID / HpcE protein / Mycobacerium smegmatis / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homologyFumarylacetoacetate hydrolase; domain 2 / Fumarylacetoacetase-like, C-terminal domain / Fumarylacetoacetase-like, C-terminal / Fumarylacetoacetase-like, C-terminal domain superfamily / Fumarylacetoacetate (FAA) hydrolase family / catalytic activity / Alpha-Beta Complex / Alpha Beta / Putative HpcE protein
Function and homology information
Biological speciesMycolicibacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of a putative HpcE protein from Mycobacterium smegmatis
Authors: Abendroth, J. / Horanyi, P.S. / Lorimer, D.D. / Edwards, T.E.
History
DepositionDec 7, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative HpcE protein
B: Putative HpcE protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,59216
Polymers63,4792
Non-polymers1,11414
Water8,341463
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4830 Å2
ΔGint-191 kcal/mol
Surface area20890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.250, 68.250, 218.980
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11B-210-

ARG

21B-591-

HOH

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Components

#1: Protein Putative HpcE protein


Mass: 31739.320 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / Gene: MSMEG_2007 / Plasmid: MysmA.00471.a.AE1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: A0QTY3
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 463 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.32 Å3/Da / Density % sol: 47.1 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 22 mg/mL MysmA.00471.a.AE1.PW38681 against Microlytic/Anatrace MCSG-1 screen condition H7 (2000 mM ammonium sulfate, 100 mM Bis-Tris/HCl, pH 5.5), cryoprotectant: 25% ethylene glycol in 2 ...Details: 22 mg/mL MysmA.00471.a.AE1.PW38681 against Microlytic/Anatrace MCSG-1 screen condition H7 (2000 mM ammonium sulfate, 100 mM Bis-Tris/HCl, pH 5.5), cryoprotectant: 25% ethylene glycol in 2 steps, tray 311974h7, puck uac1-9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Nov 25, 2019
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.75→45.93 Å / Num. obs: 60836 / % possible obs: 100 % / Redundancy: 7.276 % / Biso Wilson estimate: 31.31 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.053 / Rrim(I) all: 0.057 / Χ2: 1.027 / Net I/σ(I): 20.89 / Num. measured all: 442650 / Scaling rejects: 11
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.75-1.87.360.4923.9632590442844280.9310.53100
1.8-1.847.380.394.8531897432243220.9610.42100
1.84-1.97.3940.2986.3730899417941790.9730.32100
1.9-1.967.3790.2198.4830159408840870.9890.236100
1.96-2.027.4030.1879.7629169394139400.9880.201100
2.02-2.097.3810.14912.1628108380838080.9920.16100
2.09-2.177.3790.11415.2227642374637460.9950.123100
2.17-2.267.3660.09817.726341357635760.9960.106100
2.26-2.367.3480.08320.4425453346434640.9970.089100
2.36-2.477.3390.07422.823968326632660.9970.08100
2.47-2.617.3230.06325.9323163316431630.9980.068100
2.61-2.777.2840.05728.5321517295429540.9980.061100
2.77-2.967.2140.04733.0220611285728570.9990.051100
2.96-3.27.2140.04337.818714259525940.9990.046100
3.2-3.57.0950.03841.2417242243224300.9990.04199.9
3.5-3.917.0550.03643.7715577220822080.9990.039100
3.91-4.527.0380.0344613963198419840.9990.037100
4.52-5.536.920.03346.1811625168016800.9990.036100
5.53-7.836.8340.03445.449281135813580.9990.036100
7.83-45.935.9730.03743.8447318127920.9980.04197.5

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.17.1refinement
PDB_EXTRACT3.25data extraction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 1I7O & 3LRK

1i7o

3lrk


Resolution: 1.75→45.93 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.11
RfactorNum. reflection% reflectionSelection details
Rfree0.2002 2083 3.43 %0
Rwork0.1598 ---
obs0.1611 60744 99.94 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 113.44 Å2 / Biso mean: 31.9973 Å2 / Biso min: 12.58 Å2
Refinement stepCycle: final / Resolution: 1.75→45.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4146 0 57 481 4684
Biso mean--70.07 39.59 -
Num. residues----550
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084376
X-RAY DIFFRACTIONf_angle_d0.9075996
X-RAY DIFFRACTIONf_dihedral_angle_d18.461575
X-RAY DIFFRACTIONf_chiral_restr0.064668
X-RAY DIFFRACTIONf_plane_restr0.006801
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.75-1.790.22611520.199938193971
1.79-1.840.24361430.204338133956
1.84-1.890.22911230.193538653988
1.89-1.940.22221590.183938564015
1.94-20.24431370.178338483985
2-2.070.19981460.175338634009
2.07-2.160.18991350.159938423977
2.16-2.260.21551500.156838814031
2.26-2.380.22451420.157338904032
2.38-2.520.21581220.160139274049
2.52-2.720.23991340.168139154049
2.72-2.990.21971420.168439274069
2.99-3.420.18061300.159339774107
3.43-4.310.17431190.139140344153
4.32-45.930.17581490.15142044353
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)
13.3859-1.1878-0.17365.3087-0.17086.4458-0.1608-0.02940.19250.2817-0.04320.2661-0.3194-0.35720.22330.2213-0.0586-0.0250.2685-0.04230.2056-30.402415.9041-3.6665
2-0.0092-0.05150.23512.15281.85873.8936-0.06470.03010.0568-0.0341-0.02070.0864-0.3179-0.30020.07920.1669-0.07050.00280.282-0.01490.2299-30.127913.3563-11.0694
31.78790.3301-0.38871.538-0.25692.1792-0.12730.2199-0.1969-0.1310.126-0.29310.1250.48920.05770.1479-0.10770.01360.4194-0.05610.2535-20.5059-3.5999-21.904
41.15630.11190.11151.6052-0.26231.0002-0.04610.0902-0.0875-0.04530.0639-0.139-0.01310.079-0.02830.134-0.09770.00520.3184-0.01610.2089-21.50630.0006-18.1911
51.86980.22240.86790.8292-0.31461.8855-0.00120.1904-0.2126-0.09910.023-0.18580.08520.30760.00550.1828-0.11110.01490.3441-0.03940.2693-16.50450.9566-20.9766
61.11051.60190.80118.94980.22282.24760.1101-0.1243-0.29810.4899-0.0835-0.48890.23870.3575-0.04540.1428-0.0765-0.0570.40850.02760.3047-14.5749-7.448-6.6333
72.4355-2.1623-1.48534.7945-0.79752.5102-0.11030.13060.22870.08750.04080.052-0.27130.0780.06620.1879-0.1198-0.03580.3394-0.0140.2393-57.40112.572-21.1434
82.9103-0.1481-0.490.84780.60481.214-0.0693-0.02170.0201-0.0440.11220.283-0.1484-0.212-0.03960.1665-0.0899-0.02510.41590.01380.3034-63.0626-1.161-19.5315
90.95920.13640.08320.7717-0.28910.9689-0.0870.2175-0.0472-0.16050.1043-0.03880.1231-0.0065-0.00710.2088-0.1370.0150.354-0.01990.2154-39.2307-9.5004-30.4229
103.4563-0.81491.74672.1661.22722.2317-0.0361-0.1277-0.31430.25580.25060.26420.2518-0.3357-0.19070.1613-0.143-0.00220.2986-0.01050.2139-48.773-15.1903-21.2583
110.64650.22950.24811.032-0.09961.101-0.07620.2101-0.0713-0.1690.113-0.07590.09970.0883-0.03480.2093-0.1350.00820.3693-0.02870.2181-41.4276-12.9062-32.0061
121.9276-0.5859-0.88721.07120.24641.51060.07960.4310.0639-0.212-0.0112-0.09860.0182-0.0289-0.07890.2692-0.1527-0.01480.48340.02020.2301-43.377-7.3567-45.4351
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 32 )A1 - 32
2X-RAY DIFFRACTION2chain 'A' and (resid 33 through 76 )A33 - 76
3X-RAY DIFFRACTION3chain 'A' and (resid 77 through 109 )A77 - 109
4X-RAY DIFFRACTION4chain 'A' and (resid 110 through 195 )A110 - 195
5X-RAY DIFFRACTION5chain 'A' and (resid 196 through 248 )A196 - 248
6X-RAY DIFFRACTION6chain 'A' and (resid 249 through 277 )A249 - 277
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 39 )B1 - 39
8X-RAY DIFFRACTION8chain 'B' and (resid 40 through 59 )B40 - 59
9X-RAY DIFFRACTION9chain 'B' and (resid 60 through 136 )B60 - 136
10X-RAY DIFFRACTION10chain 'B' and (resid 137 through 151 )B137 - 151
11X-RAY DIFFRACTION11chain 'B' and (resid 152 through 248 )B152 - 248
12X-RAY DIFFRACTION12chain 'B' and (resid 249 through 279 )B249 - 279

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