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- PDB-6q09: Crystal structure of iron-bound Hemerythrin HHE cation binding do... -

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Basic information

Entry
Database: PDB / ID: 6q09
TitleCrystal structure of iron-bound Hemerythrin HHE cation binding domain-containing protein: 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: 1.75 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Biochem.J. / Year: 2020
Title: Crystal structure of a hemerythrin-like protein from Mycobacterium kansasii and homology model of the orthologous Rv2633c protein of M. tuberculosis.
Authors: Ma, Z. / Abendroth, J. / Buchko, G.W. / Rohde, K.H. / Davidson, V.L.
History
DepositionAug 1, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)19,6453
Polymers19,5331
Non-polymers1122
Water1,982110
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)52.490, 52.490, 104.420
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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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-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 2.13 Å3/Da / Density % sol: 42.28 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: Optimization screen around condition MCSG1-H6, well G8: 3.64M sodium formate, 100mM Sodium acetate / HCl pH 4.89: MykaA.20209.a.B11.PB00104 at 22mg/ml, iron-containing red protein: harvest ...Details: Optimization screen around condition MCSG1-H6, well G8: 3.64M sodium formate, 100mM Sodium acetate / HCl pH 4.89: MykaA.20209.a.B11.PB00104 at 22mg/ml, iron-containing red protein: harvest after 15h: cryo: direct: tray 310977 a7: puck ydb7-1

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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: 1.75→45.458 Å / Num. obs: 17427 / % possible obs: 99.9 % / Redundancy: 10.704 % / Biso Wilson estimate: 37.953 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.045 / Rrim(I) all: 0.047 / Χ2: 1.045 / Net I/σ(I): 26.56 / Num. measured all: 186546 / Scaling rejects: 12
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
1.75-1.810.9720.6213.6613550124012350.9720.65299.6
1.8-1.8410.9020.4764.6513519124312400.9820.599.8
1.84-1.910.8760.3426.4112997119711950.9890.35999.8
1.9-1.9610.990.2658.1512705115911560.9960.27999.7
1.96-2.0210.9230.18311.2212572115111510.9970.192100
2.02-2.0910.8880.13715.0211879109110910.9980.144100
2.09-2.1710.910.10618.9611652106810680.9980.112100
2.17-2.2610.8360.08323.11108149999980.9990.08799.9
2.26-2.3610.8650.07426.68106809839830.9990.077100
2.36-2.4810.8140.0632.1103499579570.9990.063100
2.48-2.6110.8290.05535.2197469009000.9990.058100
2.61-2.7710.7240.04940.592558638630.9990.052100
2.77-2.9610.6760.04545.284987967960.9990.047100
2.96-3.210.590.04149.0678797447440.9990.043100
3.2-3.510.4470.03753.175537237230.9990.039100
3.5-3.9110.3720.03455.4365036276270.9990.035100
3.91-4.5210.2510.03357.4258335695690.9990.034100
4.52-5.5310.0340.03155.57501750050010.033100
5.53-7.839.6040.03455.1837843943940.9990.036100
7.83-45.4587.430.03648.5517612462370.9980.03996.3

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX(dev_3500)refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Apo structure, PDB entry 6pie

6pie
PDB Unreleased entry


Resolution: 1.75→45.458 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.07
RfactorNum. reflection% reflectionSelection details
Rfree0.2245 1802 10.4 %0
Rwork0.1832 ---
obs0.1875 17335 99.57 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 91.48 Å2 / Biso mean: 40.2846 Å2 / Biso min: 20.92 Å2
Refinement stepCycle: final / Resolution: 1.75→45.458 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1289 0 2 114 1405
Biso mean--33.62 44.36 -
Num. residues----162
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091357
X-RAY DIFFRACTIONf_angle_d0.9271852
X-RAY DIFFRACTIONf_dihedral_angle_d18.544856
X-RAY DIFFRACTIONf_chiral_restr0.053210
X-RAY DIFFRACTIONf_plane_restr0.007245
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7501-1.79750.30221380.257114299
1.7975-1.85030.32461050.2463119499
1.8503-1.91010.34991570.2265113899
1.9101-1.97830.28811020.2235122399
1.9783-2.05750.29861610.2041142100
2.0575-2.15120.24161430.20441173100
2.1512-2.26460.23731600.2011116399
2.2646-2.40650.24951400.19421182100
2.4065-2.59230.23551440.19211201100
2.5923-2.85310.21891180.20271223100
2.8531-3.26580.23741540.20191210100
3.2658-4.11420.17861530.16521212100
4.1142-45.450.21121270.15331330100
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)
16.0361-4.26726.32093.6846-4.67847.4276-0.7008-0.869-0.04240.84680.75690.2198-1.2414-1.2247-0.01550.47150.16140.08180.43060.03430.3291-10.647141.98526.3808
25.8606-1.6664.31812.7761-2.55085.86390.2159-0.0599-0.0921-0.08970.01820.0760.38840.0485-0.12230.303-0.01730.02180.4110.00240.1909-8.0729.8695-7.4975
36.823-3.72324.37313.3972-3.41765.54490.1994-0.6064-0.40910.03520.4460.48270.0089-0.9155-0.54470.2051-0.00270.03070.39370.07230.2718-14.182230.91155.959
41.5101-1.78561.94313.2124-3.04334.359-0.0576-0.00110.14350.0698-0.001-0.1292-0.1813-0.03430.06540.2244-0.0080.02780.27450.00120.2131-4.203237.0142.0481
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 89 through 123 )A89 - 123
2X-RAY DIFFRACTION2chain 'A' and (resid 124 through 161 )A124 - 161
3X-RAY DIFFRACTION3chain 'A' and (resid 0 through 28 )A0 - 28
4X-RAY DIFFRACTION4chain 'A' and (resid 29 through 88 )A29 - 88

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