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- PDB-1nlx: Crystal Structure of PHL P 6, A Major Timothy Grass Pollen Allerg... -

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Entry
Database: PDB / ID: 1nlx
TitleCrystal Structure of PHL P 6, A Major Timothy Grass Pollen Allergen Co-Crystallized with Zinc
ComponentsPollen allergen Phl p 6
KeywordsALLERGEN / Allergen Phl p 6 / four-helix-bundle / Structural Genomics / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homologyGroup V grass pollen allergen / Pollen allergen Poa p IX/Phl p VI / Pollen allergen/Uncharacterized protein Os / Ribonuclease (pollen allergen) / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha / ARSENIC / Pollen allergen Phl p 6
Function and homology information
Biological speciesPhleum pratense (timothy grass)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsFedorov, A.A. / Ball, T. / Fedorov, E.V. / Vrtala, S. / Valenta, R. / Almo, S.C. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
Citation
Journal: To be Published
Title: Crystal Structure oh Phl p 6, a major timothy grass pollen allergen co-crystallized with Zinc
Authors: Fedorov, A.A. / Ball, T. / Fedorov, E.V. / Vrtala, S. / Valenta, R. / Almo, S.C.
#1: Journal: J.Immunol. / Year: 1999
Title: Molecular, Immunological, and Structural Characterization of Phl p 6, a Major Allergen and P-Particle-Associated Protein from Timothy Grass (Phleum pratense) Pollen
Authors: Vrtala, S. / Fischer, S. / Grote, M. / Vangelista, L. / Pastore, A. / Sperr, W.R. / Valent, P. / Reichelt, R. / Kraft, D. / Valenta, R.
#2: Journal: Int.Arch.Allergy.Immunol / Year: 1997
Title: X-ray crystal structures of birch pollen profilin and Phl p 2
Authors: Fedorov, A.A. / Ball, T. / Valenta, R. / Almo, S.C.
#3: Journal: Structure / Year: 1997
Title: The molecular basis for allergen cross-reactivity: crystal structure and IGE-epitope mapping of birch pollen profilin
Authors: Fedorov, A.A. / Ball, T. / Mahoney, N.M. / Valenta, R. / Almo, S.C.
History
DepositionJan 7, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / pdbx_struct_conn_angle ...audit_author / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _pdbx_struct_conn_angle.ptnr1_auth_asym_id ..._audit_author.identifier_ORCID / _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 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pollen allergen Phl p 6
B: Pollen allergen Phl p 6
C: Pollen allergen Phl p 6
D: Pollen allergen Phl p 6
E: Pollen allergen Phl p 6
F: Pollen allergen Phl p 6
G: Pollen allergen Phl p 6
H: Pollen allergen Phl p 6
I: Pollen allergen Phl p 6
J: Pollen allergen Phl p 6
K: Pollen allergen Phl p 6
L: Pollen allergen Phl p 6
M: Pollen allergen Phl p 6
N: Pollen allergen Phl p 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,46549
Polymers167,11014
Non-polymers2,35635
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Pollen allergen Phl p 6
N: Pollen allergen Phl p 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2097
Polymers23,8732
Non-polymers3375
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-123 kcal/mol
Surface area11010 Å2
MethodPISA
3
B: Pollen allergen Phl p 6
hetero molecules

H: Pollen allergen Phl p 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2097
Polymers23,8732
Non-polymers3375
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_455x-1/2,-y+1/2,-z1
Buried area1900 Å2
ΔGint-123 kcal/mol
Surface area10970 Å2
MethodPISA
4
I: Pollen allergen Phl p 6
M: Pollen allergen Phl p 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2097
Polymers23,8732
Non-polymers3375
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-123 kcal/mol
Surface area11050 Å2
MethodPISA
5
D: Pollen allergen Phl p 6
F: Pollen allergen Phl p 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2097
Polymers23,8732
Non-polymers3375
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1900 Å2
ΔGint-122 kcal/mol
Surface area11080 Å2
MethodPISA
6
G: Pollen allergen Phl p 6
K: Pollen allergen Phl p 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2097
Polymers23,8732
Non-polymers3375
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-122 kcal/mol
Surface area10950 Å2
MethodPISA
7
E: Pollen allergen Phl p 6
L: Pollen allergen Phl p 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2097
Polymers23,8732
Non-polymers3375
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-121 kcal/mol
Surface area11140 Å2
MethodPISA
8
I: Pollen allergen Phl p 6
J: Pollen allergen Phl p 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2097
Polymers23,8732
Non-polymers3375
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1190 Å2
ΔGint-105 kcal/mol
Surface area11790 Å2
MethodPISA, PQS
9
C: Pollen allergen Phl p 6
D: Pollen allergen Phl p 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2848
Polymers23,8732
Non-polymers4116
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1190 Å2
ΔGint-103 kcal/mol
Surface area11820 Å2
MethodPISA, PQS
10
K: Pollen allergen Phl p 6
L: Pollen allergen Phl p 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2848
Polymers23,8732
Non-polymers4116
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1190 Å2
ΔGint-104 kcal/mol
Surface area11740 Å2
MethodPISA, PQS
11
E: Pollen allergen Phl p 6
F: Pollen allergen Phl p 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1346
Polymers23,8732
Non-polymers2624
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint-102 kcal/mol
Surface area11810 Å2
MethodPISA, PQS
12
A: Pollen allergen Phl p 6
B: Pollen allergen Phl p 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2097
Polymers23,8732
Non-polymers3375
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint-103 kcal/mol
Surface area11690 Å2
MethodPISA, PQS
13
G: Pollen allergen Phl p 6
H: Pollen allergen Phl p 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1346
Polymers23,8732
Non-polymers2624
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint-102 kcal/mol
Surface area11710 Å2
MethodPISA, PQS
14
M: Pollen allergen Phl p 6
N: Pollen allergen Phl p 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2097
Polymers23,8732
Non-polymers3375
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1150 Å2
ΔGint-103 kcal/mol
Surface area11780 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)110.809, 110.335, 159.420
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Pollen allergen Phl p 6 / Phl p VI


Mass: 11936.394 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phleum pratense (timothy grass) / Gene: PHLPVI / Production host: Escherichia coli (E. coli) / References: UniProt: P43215
#2: Chemical...
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-ARS / ARSENIC


Mass: 74.922 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: As

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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: 2.851 Å3/Da / Density % sol: 55.19 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: ammonium sulfate, cacodylate, Zn acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 278K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9A / Wavelength: 0.98 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 1, 2002 / Details: Mirrors
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. all: 46387 / Num. obs: 46387 / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 26.6
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.266 / Mean I/σ(I) obs: 7.2 / % possible all: 93.5

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNS1refinement
RefinementMethod to determine structure: MAD / Resolution: 2.8→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.272 2305 4.7 %RANDOM
Rwork0.243 ---
all0.248 46387 --
obs0.248 46387 --
Solvent computationBsol: 11.0385 Å2 / ksol: 0.283555 e/Å3
Displacement parametersBiso mean: 42.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.47 Å0.42 Å
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11116 0 35 0 11151
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.27
X-RAY DIFFRACTIONc_dihedral_angle_d18.1
X-RAY DIFFRACTIONc_improper_angle_d0.91
X-RAY DIFFRACTIONc_mcbond_it5.291.5
X-RAY DIFFRACTIONc_mcangle_it8.552
X-RAY DIFFRACTIONc_scbond_it10.512
X-RAY DIFFRACTIONc_scangle_it15.292.5
LS refinement shellResolution: 2.8→2.9 Å / Rfactor Rfree error: 0.006 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.339 216 5 %
Rwork0.312 4295 -
obs--95.3 %

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