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- PDB-7tmv: Crystal structure of a Putative structural protein from Klebsiell... -

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Basic information

Entry
Database: PDB / ID: 7tmv
TitleCrystal structure of a Putative structural protein from Klebsiella pneumoniae
ComponentsPutative structural protein
KeywordsMETAL BINDING PROTEIN / structural protein / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE
Function / homologyProtein of unknown function DUF892, YciF-like / Domain of unknown function (DUF892) / Ferritin-like / Ferritin-like superfamily / Putative structural protein
Function and homology information
Biological speciesKlebsiella pneumoniae subsp. pneumoniae HS11286 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700059C United States
CitationJournal: To be published
Title: Crystal structure of a Putative structural protein from Klebsiella pneumoniae
Authors: Liu, L. / Lovell, S. / Battaile, K.P. / Tillery, L. / Shek, R. / Craig, J.K. / Barrett, L.K. / Van Voorhis, W.C.
History
DepositionJan 20, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)38,8226
Polymers38,5602
Non-polymers2624
Water52229
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2940 Å2
ΔGint-179 kcal/mol
Surface area13230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.227, 104.652, 45.889
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 11 through 33 or (resid 34...
21(chain B and (resid 11 or (resid 12 and (name...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETTHRTHR(chain A and (resid 11 through 33 or (resid 34...AA11 - 3311 - 33
12ARGARGARGARG(chain A and (resid 11 through 33 or (resid 34...AA3434
13METMETLYSLYS(chain A and (resid 11 through 33 or (resid 34...AA11 - 16911 - 169
14METMETLYSLYS(chain A and (resid 11 through 33 or (resid 34...AA11 - 16911 - 169
15METMETLYSLYS(chain A and (resid 11 through 33 or (resid 34...AA11 - 16911 - 169
16METMETLYSLYS(chain A and (resid 11 through 33 or (resid 34...AA11 - 16911 - 169
21METMETMETMET(chain B and (resid 11 or (resid 12 and (name...BB1111
22LYSLYSLYSLYS(chain B and (resid 11 or (resid 12 and (name...BB1212
23ASNASNGLYGLY(chain B and (resid 11 or (resid 12 and (name...BB10 - 16410 - 164
24ASNASNGLYGLY(chain B and (resid 11 or (resid 12 and (name...BB10 - 16410 - 164
25ASNASNGLYGLY(chain B and (resid 11 or (resid 12 and (name...BB10 - 16410 - 164
26ASNASNGLYGLY(chain B and (resid 11 or (resid 12 and (name...BB10 - 16410 - 164

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Components

#1: Protein Putative structural protein


Mass: 19279.934 Da / Num. of mol.: 2 / Fragment: KlpnC.20486.a.B1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae HS11286 (bacteria)
Strain: HS11286 / Gene: KPHS_20300 / Plasmid: KlpnC.20486.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H3GMY9
#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.: 29 / 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: 1.94 Å3/Da / Density % sol: 36.52 % / Mosaicity: 0.13 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Morpheus F1: 12% (v/v) PEG 500 MME, 6% (w/v) PEG 20,000, 0.05 M imidazole, 0.05 M MES, 0.02 M each of D-glucose, D-mannose, D-galactose, L-fucose, D-xylose and N-acetyl-D-glucosamine, KlpnC. ...Details: Morpheus F1: 12% (v/v) PEG 500 MME, 6% (w/v) PEG 20,000, 0.05 M imidazole, 0.05 M MES, 0.02 M each of D-glucose, D-mannose, D-galactose, L-fucose, D-xylose and N-acetyl-D-glucosamine, KlpnC.20486.a.B1.PW39078 at 5 mg/mL, Tray: plate 12355 well F1 drop 1, Puck: PSL1206, Cryo: direct

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.984 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 2.3→62.23 Å / Num. obs: 13864 / % possible obs: 99.7 % / Redundancy: 6.4 % / Biso Wilson estimate: 42.89 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.122 / Net I/σ(I): 9.8 / Num. measured all: 88737 / Scaling rejects: 8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Net I/σ(I) obs% possible all
2.3-2.386.81.112900613270.7151.999.9
8.91-62.235.70.04315892810.99926.696.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.7data scaling
MOLREPphasing
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GS4

2gs4


Resolution: 2.3→52.33 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2669 642 4.65 %
Rwork0.2255 13171 -
obs0.2275 13813 99.43 %
Solvent computationShrinkage radii: 0.85 Å / VDW probe radii: 1.22 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 109.92 Å2 / Biso mean: 52.2841 Å2 / Biso min: 28.42 Å2
Refinement stepCycle: final / Resolution: 2.3→52.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2317 0 4 29 2350
Biso mean--72.55 43.77 -
Num. residues----314
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1312X-RAY DIFFRACTION6.194TORSIONAL
12B1312X-RAY DIFFRACTION6.194TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.480.34061190.270925962715100
2.48-2.730.32971290.274325832712100
2.73-3.120.28621270.263826122739100
3.12-3.930.29441260.216526472773100
3.93-52.330.21961410.19852733287498
Refinement TLS params.Method: refined / Origin x: 5.816 Å / Origin y: 25.442 Å / Origin z: 14.243 Å
111213212223313233
T0.3065 Å2-0.0157 Å20.0305 Å2-0.2583 Å2-0.1191 Å2--0.3548 Å2
L2.4144 °20.7923 °20.044 °2-2.2309 °2-0.6538 °2--1.4132 °2
S0.021 Å °-0.2217 Å °0.6233 Å °0.0434 Å °-0.0044 Å °0.1491 Å °-0.0022 Å °0.0684 Å °-0.0087 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 11:169 OR RESID 201:202 ) ) OR ( CHAIN B AND ( RESID 10:164 OR RESID 201:202 ) )A11 - 169
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 11:169 OR RESID 201:202 ) ) OR ( CHAIN B AND ( RESID 10:164 OR RESID 201:202 ) )A201 - 202
3X-RAY DIFFRACTION1( CHAIN A AND ( RESID 11:169 OR RESID 201:202 ) ) OR ( CHAIN B AND ( RESID 10:164 OR RESID 201:202 ) )B10 - 164
4X-RAY DIFFRACTION1( CHAIN A AND ( RESID 11:169 OR RESID 201:202 ) ) OR ( CHAIN B AND ( RESID 10:164 OR RESID 201:202 ) )B201 - 202

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