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- PDB-1jcc: Crystal Structure of a Novel Alanine-Zipper Trimer at 1.7 A Resol... -

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Basic information

Entry
Database: PDB / ID: 1jcc
TitleCrystal Structure of a Novel Alanine-Zipper Trimer at 1.7 A Resolution, V13A,L16A,V20A,L23A,V27A,M30A,V34A mutations
ComponentsMAJOR OUTER MEMBRANE LIPOPROTEIN
KeywordsMEMBRANE PROTEIN / LIPOPROTEIN / PROTEIN FOLDING / COILED COIL / HELIX CAPPING / ALANINE-ZIPPER
Function / homology
Function and homology information


periplasmic space organization / lipid modification / peptidoglycan binding / cell outer membrane / outer membrane-bounded periplasmic space / lipid binding / extracellular region / identical protein binding / membrane
Similarity search - Function
Lipoprotein leucine-zipper / Major outer membrane lipoprotein Lpp / Lipoprotein leucine-zipper / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #190 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Prokaryotic membrane lipoprotein lipid attachment site profile. / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Major outer membrane lipoprotein Lpp
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsLiu, J. / Dai, J. / Lu, M.
CitationJournal: Biochemistry / Year: 2003
Title: Zinc-Mediated Helix Capping in A Triple-Helical Protein
Authors: Liu, J. / Dai, J. / Lu, M.
History
DepositionJun 8, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _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.ptnr1_symmetry / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MAJOR OUTER MEMBRANE LIPOPROTEIN
B: MAJOR OUTER MEMBRANE LIPOPROTEIN
C: MAJOR OUTER MEMBRANE LIPOPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9126
Polymers17,7163
Non-polymers1963
Water4,216234
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5650 Å2
ΔGint-101 kcal/mol
Surface area8700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.388, 33.322, 71.979
Angle α, β, γ (deg.)90.00, 102.55, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly is a trimer.

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Components

#1: Protein MAJOR OUTER MEMBRANE LIPOPROTEIN / MUREIN-LIPOPROTEIN


Mass: 5905.234 Da / Num. of mol.: 3 / Mutation: V13A,L16A,V20A,L23A,V27A,M30A,V34A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P69776
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 234 / Source method: isolated from a natural source / Formula: H2O

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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: 2.06 Å3/Da / Density % sol: 40.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: Sodium acetate, zinc acetate, PEG 8000, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
250 mMzinc acetate1drop
30.1 Msodium acetate1reservoirpH5.6
40.1 Mzinc acetate1reservoir
518 %PEG80001reservoir

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.1 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 20, 2000
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 15821 / Num. obs: 15821 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 21.9 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 7.7
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.383 / Mean I/σ(I) obs: 3.3 / Num. unique all: 1605 / % possible all: 97.6
Reflection
*PLUS
Lowest resolution: 50 Å / Num. measured all: 69970

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Processing

Software
NameVersionClassification
MADNESSdata collection
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
MADNESSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EQ7

1eq7


Resolution: 1.7→35.13 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1029074.03 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.223 1594 10.1 %RANDOM
Rwork0.192 ---
all-15821 --
obs-15821 97.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 73.9 Å2 / ksol: 0.408 e/Å3
Displacement parametersBiso mean: 22.1 Å2
Baniso -1Baniso -2Baniso -3
1-7.56 Å20 Å20.45 Å2
2---1.56 Å20 Å2
3----5.99 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 1.7→35.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1094 0 3 234 1331
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg0.9
X-RAY DIFFRACTIONc_dihedral_angle_d15.5
X-RAY DIFFRACTIONc_improper_angle_d0.68
X-RAY DIFFRACTIONc_mcbond_it1.171.5
X-RAY DIFFRACTIONc_mcangle_it1.622
X-RAY DIFFRACTIONc_scbond_it2.552
X-RAY DIFFRACTIONc_scangle_it3.672.5
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.299 252 9.6 %
Rwork0.25 2360 -
obs-2612 98.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 50 Å / Num. reflection obs: 14227
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg15.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.68

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