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- PDB-4pnj: Recombinant Sperm Whale P6 Myoglobin Solved with Single Pulse Fre... -

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Basic information

Entry
Database: PDB / ID: 4pnj
TitleRecombinant Sperm Whale P6 Myoglobin Solved with Single Pulse Free Electron Laser Data
ComponentsMyoglobin
KeywordsOXYGEN TRANSPORT / Myoglobin / Femtosecond X-ray Crystallography
Function / homology
Function and homology information


hydrogen peroxide mediated signaling pathway / oxygen carrier activity / oxygen binding / heme binding / metal ion binding
Similarity search - Function
Myoglobin / Globins / Globin family profile. / Globin-like / Globin / Globin / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Myoglobin
Similarity search - Component
Biological speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.36 Å
Model detailsStructure solved from data obtained from 739 crystals
AuthorsCohen, A. / Gonzalez, A. / Lam, W. / Lyubimov, A. / Sauter, N. / Tsai, Y. / Uervirojnangkoorn, M. / Brunger, A. / Soltis, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Goniometer-based femtosecond crystallography with X-ray free electron lasers.
Authors: Cohen, A.E. / Soltis, S.M. / Gonzalez, A. / Aguila, L. / Alonso-Mori, R. / Barnes, C.O. / Baxter, E.L. / Brehmer, W. / Brewster, A.S. / Brunger, A.T. / Calero, G. / Chang, J.F. / Chollet, M. ...Authors: Cohen, A.E. / Soltis, S.M. / Gonzalez, A. / Aguila, L. / Alonso-Mori, R. / Barnes, C.O. / Baxter, E.L. / Brehmer, W. / Brewster, A.S. / Brunger, A.T. / Calero, G. / Chang, J.F. / Chollet, M. / Ehrensberger, P. / Eriksson, T.L. / Feng, Y. / Hattne, J. / Hedman, B. / Hollenbeck, M. / Holton, J.M. / Keable, S. / Kobilka, B.K. / Kovaleva, E.G. / Kruse, A.C. / Lemke, H.T. / Lin, G. / Lyubimov, A.Y. / Manglik, A. / Mathews, I.I. / McPhillips, S.E. / Nelson, S. / Peters, J.W. / Sauter, N.K. / Smith, C.A. / Song, J. / Stevenson, H.P. / Tsai, Y. / Uervirojnangkoorn, M. / Vinetsky, V. / Wakatsuki, S. / Weis, W.I. / Zadvornyy, O.A. / Zeldin, O.B. / Zhu, D. / Hodgson, K.O.
History
DepositionMay 23, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 5, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 3, 2014Group: Database references
Revision 1.2Dec 17, 2014Group: Database references
Revision 1.3Apr 1, 2015Group: Other
Revision 1.4Nov 18, 2015Group: Data collection
Revision 1.5Nov 15, 2017Group: Data collection / Derived calculations / Refinement description
Category: diffrn_source / pdbx_struct_oper_list / software
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.type / _pdbx_struct_oper_list.symmetry_operation
Revision 1.6Nov 28, 2018Group: Data collection
Category: diffrn / pdbx_serial_crystallography_data_reduction ...diffrn / pdbx_serial_crystallography_data_reduction / pdbx_serial_crystallography_measurement / pdbx_serial_crystallography_sample_delivery_fixed_target
Item: _diffrn.pdbx_serial_crystal_experiment
Revision 1.7Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,75110
Polymers17,3661
Non-polymers1,3859
Water6,485360
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2220 Å2
ΔGint-95 kcal/mol
Surface area8270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.309, 90.309, 45.204
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number168
Space group name H-MP6
Components on special symmetry positions
IDModelComponents
11A-207-

SO4

21A-427-

HOH

31A-429-

HOH

41A-508-

HOH

Detailsbiological unit is the same as asym.

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Components

#1: Protein Myoglobin /


Mass: 17366.148 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physeter catodon (sperm whale) / Gene: MB / Production host: Escherichia coli (E. coli) / References: UniProt: P02185
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 360 / 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: 3.06 Å3/Da / Density % sol: 59.86 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 2.2 - 2.8M (NH4)2SO4 in 20mM TrisHCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: XPP
Details: The data was assembled from still diffraction patterns collected from 739 crystals at the LCLS beamline XPP, using 50fs pulses
Wavelength: 1.31 Å
DetectorType: CS-PAD CXI-1 / Detector: PIXEL / Date: Dec 7, 2012
RadiationMonochromator: None (SASE pulse) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.31 Å / Relative weight: 1
ReflectionResolution: 1.36→39.15 Å / Num. obs: 43767 / % possible obs: 95.7 % / Redundancy: 25.1 % / Biso Wilson estimate: 15.24 Å2 / Net I/σ(I): 33.94
Reflection shellResolution: 1.36→1.37 Å / % possible obs: 52 % / Redundancy: 1.57 % / % possible all: 52
Serial crystallography measurementFocal spot size: 50 µm2 / Photons per pulse: 1 Tphotons/pulse / Pulse duration: 30 fsec. / Pulse photon energy: 9.5 keV
Serial crystallography sample delivery fixed targetMotion control: DCSS / Sample holding: polycarbonate grid
Sample solvent: 8% NaCl, 0.1M Sodium Acetage pH 4.0, 100mM Gadoteridol
Support base: goniometer
Serial crystallography data reductionCrystal hits: 932 / Frames indexed: 739 / Frames total: 932

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
cctbx.xfeldata reduction
MOLREP11.0.05phasing
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: 1.9_1692)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VXA

1vxa


Resolution: 1.36→39.105 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 2.15 / Phase error: 18.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1881 2585 5.91 %
Rwork0.1586 41144 -
obs0.1603 43729 95.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 54.79 Å2 / Biso mean: 20.7716 Å2 / Biso min: 11.01 Å2
Refinement stepCycle: final / Resolution: 1.36→39.105 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1222 0 113 364 1699
Biso mean--18.76 31.71 -
Num. residues----154
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131467
X-RAY DIFFRACTIONf_angle_d1.4322008
X-RAY DIFFRACTIONf_chiral_restr0.087199
X-RAY DIFFRACTIONf_plane_restr0.008251
X-RAY DIFFRACTIONf_dihedral_angle_d15.506540
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.36-1.38210.389830.38491310139355
1.3821-1.41030.37131180.3511810192876
1.4103-1.4410.34811310.30652185231692
1.441-1.47450.27731480.25242322247099
1.4745-1.51140.24311510.209123922543100
1.5114-1.55220.2311510.198223842535100
1.5522-1.59790.18521470.178423662513100
1.5979-1.64950.1971500.171623602510100
1.6495-1.70850.17931520.161523822534100
1.7085-1.77690.19741470.160323852532100
1.7769-1.85770.18031520.157123762528100
1.8577-1.95570.18021450.153123732518100
1.9557-2.07820.18731560.145323962552100
2.0782-2.23860.14641470.13524012548100
2.2386-2.46390.15841490.132324062555100
2.4639-2.82030.19411540.142723902544100
2.8203-3.55290.18171500.146524152565100
3.5529-39.12120.17411540.149124912645100
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)
10.0619-0.0657-0.00460.06450.00890.1533-0.017-0.0769-0.06230.08940.059-0.04050.07690.126100.15390.00060.00670.1647-0.00620.1375-10.765399.44164.5983
20.0664-0.0134-0.03660.01740.04680.0840.04180.2233-0.11830.10910.0416-0.08570.08750.111900.13180.0017-0.00220.1477-0.01150.1486-14.0256100.1609-14.5982
30.0952-0.0242-0.04980.08970.02620.11090.07860.16390.0398-0.1611-0.0430.039-0.0124-0.2563-0.00010.17120.0147-0.0060.2399-0.01380.1569-24.553102.7245-21.1408
40.01870.00750.00140.02110.02390.0290.1420.0338-0.1515-0.0449-0.0929-0.10710.12980.3565-0.00020.19020.03210.01740.26390.0210.141-13.0682103.0289-23.8537
50.1014-0.02750.07560.0604-0.01730.0531-0.02970.06110.0291-0.04120.026-0.01670.02940.026800.126-0.00160.00490.15250.00510.1381-15.9148109.022-8.4933
60.0772-0.0581-0.03170.14930.06490.0223-0.0346-0.06860.0370.0943-0.03240.06340.051-0.084-00.14420.00720.00380.1535-0.00660.1606-26.9419108.4581.8428
70.0021-0.0037-0.00860.01140.01390.02740.12470.266-0.0633-0.2843-0.01090.258-0.1255-0.3876-0.00010.1990.01340.00170.2487-0.01270.2033-32.1797105.5351-11.147
80.0931-0.0849-0.12960.07980.10890.29960.0156-0.0358-0.1169-0.0192-0.03260.02970.0618-0.022300.1387-0.00070.00790.1419-0.0050.1624-15.195894.0864-7.5776
90.09810.0303-0.10660.08470.00960.1414-0.0494-0.0905-0.23540.11510.03910.20410.0444-0.095-0.00010.14350.00990.01730.14760.00150.183-26.870698.05231.0034
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 19 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 20 through 35 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 36 through 51 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 52 through 58 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 59 through 78 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 79 through 95 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 96 through 100 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 101 through 124 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 125 through 153 )A0

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