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- PDB-6tyj: Crystal structure of zinc-bound Hemerythrin HHE cation binding do... -

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Basic information

Entry
Database: PDB / ID: 6tyj
TitleCrystal structure of zinc-bound Hemerythrin HHE cation binding domain-containing protein (soak): Rv2633c homolog from Mycobacterium kansasii
ComponentsHemerythrin HHE cation binding domain protein
KeywordsPROTEIN BINDING / SSGCID / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homologyHemerythrin-like / Hemerythrin HHE cation binding domain / metal ion binding / Hemerythrin HHE cation binding domain protein / Hemerythrin HHE cation binding domain protein
Function and homology information
Biological speciesMycobacterium kansasii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of zinc-bound Hemerythrin HHE cation binding domain-containing protein (soak): Rv2633c homolog from Mycobacterium kansasii
Authors: Abendroth, J. / Delker, S.L. / Buchko, G.W. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionAug 9, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 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_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemerythrin HHE cation binding domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7955
Polymers19,5331
Non-polymers2624
Water2,756153
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.230, 52.230, 104.650
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

#1: Protein Hemerythrin HHE cation binding domain protein


Mass: 19533.148 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium kansasii (bacteria) / Gene: BZL29_7639 / Plasmid: MykaA.20209.a.B11
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21(DE3) / References: UniProt: A0A1V3WIE5, UniProt: X7XZL2*PLUS
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.11 Å3/Da / Density % sol: 41.83 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: Optimization screen around condition MCSG1-H6, well C1: 3.0M sodium formate, 100mM Sodium acetate / HCl pH 4.43: MykaA.20209.a.B11.PB00104 at 22mg/ml, iron-containing red protein: O/N soak ...Details: Optimization screen around condition MCSG1-H6, well C1: 3.0M sodium formate, 100mM Sodium acetate / HCl pH 4.43: MykaA.20209.a.B11.PB00104 at 22mg/ml, iron-containing red protein: O/N soak with 5mM ZnCl2: cryo: direct: tray 311000c1: puck ydb7-6

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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: Jul 25, 2019
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 22570 / % possible obs: 100 % / Redundancy: 10.2 % / Biso Wilson estimate: 22.68 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.05 / Rrim(I) all: 0.052 / Net I/σ(I): 24.28
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.6-1.646.6930.5583.1916530.9180.605100
1.64-1.698.5940.5234.1616180.9590.55799.9
1.69-1.7410.4730.4725.3515150.9780.497100
1.74-1.7910.9310.3627.0615100.9870.3899.9
1.79-1.8510.9240.2689.2914820.9930.281100
1.85-1.9110.9460.19312.2514040.9960.203100
1.91-1.9810.8970.15615.1313730.9960.163100
1.98-2.0710.920.11119.9713400.9980.116100
2.07-2.1610.8940.08325.2912690.9990.088100
2.16-2.2610.8560.07129.2512150.9990.075100
2.26-2.3910.7880.06133.4811820.9990.064100
2.39-2.5310.8080.05338.7510700.9990.056100
2.53-2.710.7580.0541.0310420.9990.053100
2.7-2.9210.6440.04545.579920.9990.047100
2.92-3.210.4460.04248.748900.9990.044100
3.2-3.5810.3010.03752.068260.9990.039100
3.58-4.1310.2170.03353.4474110.035100
4.13-5.0610.0290.03254.336270.9990.034100
5.06-7.169.5830.03652.715090.9990.038100
7.16-507.9810.03548.963120.9980.03898.4

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Processing

Software
NameVersionClassification
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6pie, apo structure

6pie
PDB Unreleased entry


Resolution: 1.6→45.23 Å / SU ML: 0.1692 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 22.0064
RfactorNum. reflection% reflectionSelection details
Rfree0.2076 2012 8.94 %0
Rwork0.1775 ---
obs0.1802 22495 99.84 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 32.4 Å2
Refinement stepCycle: LAST / Resolution: 1.6→45.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1268 0 4 153 1425
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081320
X-RAY DIFFRACTIONf_angle_d0.89531801
X-RAY DIFFRACTIONf_chiral_restr0.0537208
X-RAY DIFFRACTIONf_plane_restr0.0074236
X-RAY DIFFRACTIONf_dihedral_angle_d16.9394821
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.25921530.22571449X-RAY DIFFRACTION99.94
1.64-1.680.27621350.22061465X-RAY DIFFRACTION99.75
1.68-1.730.28651350.21921402X-RAY DIFFRACTION99.74
1.73-1.790.25471540.20651413X-RAY DIFFRACTION99.62
1.79-1.850.24871450.20331446X-RAY DIFFRACTION99.75
1.85-1.930.22591520.18661438X-RAY DIFFRACTION99.81
1.93-2.020.2241430.18931451X-RAY DIFFRACTION99.94
2.02-2.120.24811410.18391432X-RAY DIFFRACTION99.87
2.12-2.260.21481460.18521471X-RAY DIFFRACTION99.63
2.26-2.430.21171280.17531456X-RAY DIFFRACTION99.94
2.43-2.670.19361360.1851469X-RAY DIFFRACTION100
2.67-3.060.23561480.18821500X-RAY DIFFRACTION100
3.06-3.860.2031230.16861525X-RAY DIFFRACTION100
3.86-45.230.1681730.15551566X-RAY DIFFRACTION99.77
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)
13.7875564645-2.715131060413.315547057393.50746784777-3.147591059044.189805312640.0662037599848-0.583918892472-0.2896701776860.09251396899680.5415204427780.544443491880.0438570079735-1.03104750772-0.5887397893260.1593775447910.005213999533150.02997658727840.3862482325310.1073575061180.258392016771-16.186916844932.24882156674.41064307843
22.3210384404-2.244407061192.372796985383.93658920105-3.463288122144.511173484820.08978486743390.01810140207850.00828246394381-0.1113141467080.00586468172531-0.04291011690030.147266461954-0.0885158555128-0.1422799520740.144776231-0.01535733744730.005422437023290.2089913801920.003163659681820.166117126982-6.7278171514132.32755675531.40376399942
34.74383998133-4.113661587414.282950405236.96564521461-5.54062328456.76790293971-0.1918813185490.07808302140520.2389206234160.55120562775-0.222375009404-0.500540796057-0.5967726613180.3389734745130.5289015011810.265996775791-0.0487705675645-0.03414512039930.2014066592650.03427708823530.217544984905-2.1912799817943.78217314742.50811592617
47.67082249153-4.99655510133.929395106155.24153908586-3.450863282115.48762072976-0.201315471481-0.06243535098410.5605927576840.396683648007-0.0123737229349-0.395383480039-0.761888700899-0.3369597599250.2233791720560.3332927015240.06370660015880.01310366377090.22853913265-0.01112024564030.21974012246-4.3164155202737.523108661111.9735206782
51.80514263132-1.70666640018-0.1751752350715.248415374110.3555497444712.56128320555-0.0996684621919-0.108837580976-0.119464730348-0.07608503982520.2007771740990.4052311456040.129260458323-0.23503746038-0.1065002202850.157068604787-0.0141749482186-0.01403996911730.2979557298560.05617948495790.155246769119-13.963970375334.6485000078-8.23062148963
68.76101148585-2.28228664118-2.445274388572.43748965760.2699274384634.55209104332-0.03169402830630.01257209073210.25303661873-0.716723464378-0.120470982485-0.464579525961-0.811817142812-0.2231355222070.0621291887870.4828903158410.0590773391816-0.01517865972630.6100526302450.03860588847870.3030766303574.1051986881930.451253404-1.33880855024
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 23 )
2X-RAY DIFFRACTION2chain 'A' and (resid 24 through 60 )
3X-RAY DIFFRACTION3chain 'A' and (resid 61 through 83 )
4X-RAY DIFFRACTION4chain 'A' and (resid 84 through 112 )
5X-RAY DIFFRACTION5chain 'A' and (resid 113 through 152 )
6X-RAY DIFFRACTION6chain 'A' and (resid 153 through 161 )

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