4OW3 | pdb_00004ow3

Thermolysin structure determined by free-electron laser

• PDB DOI: https://doi.org/10.2210/pdb4OW3/pdb

• Classification: HYDROLASE
• Organism(s): Bacillus thermoproteolyticus
• Mutation(s): No 


• Deposited: 2014-01-30 Released: 2014-03-12 
• Deposition Author(s): Hattne, J., Echols, N., Tran, R., Kern, J., Gildea, R.J., Brewster, A.S., Alonso-Mori, R., Glockner, C., Hellmich, J., Laksmono, H., Sierra, R.G., Lassalle-Kaiser, B., Lampe, A., Han, G., Gul, S., DiFiore, D., Milathianaki, D., Fry, A.R., Miahnahri, A., White, W.E., Schafer, D.W., Seibert, M.M., Koglin, J.E., Sokaras, D., Weng, T.-C., Sellberg, J., Latimer, M.J., Glatzel, P., Zwart, P.H., Grosse-Kunstleve, R.W., Bogan, M.J., Messerschmidt, M., Williams, G.J., Boutet, S., Messinger, J., Zouni, A., Yano, J., Bergmann, U., Yachandra, V.K., Adams, P.D., Sauter, N.K.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Department of Energy (DOE, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.263 (Depositor), 0.267 (DCC) 
• R-Value Work: 
  0.217 (Depositor), 0.225 (DCC) 
• R-Value Observed: 
  0.220 (Depositor) 

Starting Model: experimental

Literature

Accurate macromolecular structures using minimal measurements from X-ray free-electron lasers.

Hattne, J., Echols, N., Tran, R., Kern, J., Gildea, R.J., Brewster, A.S., Alonso-Mori, R., Glockner, C., Hellmich, J., Laksmono, H., Sierra, R.G., Lassalle-Kaiser, B., Lampe, A., Han, G., Gul, S., DiFiore, D., Milathianaki, D., Fry, A.R., Miahnahri, A., White, W.E., Schafer, D.W., Seibert, M.M., Koglin, J.E., Sokaras, D., Weng, T.C., Sellberg, J., Latimer, M.J., Glatzel, P., Zwart, P.H., Grosse-Kunstleve, R.W., Bogan, M.J., Messerschmidt, M., Williams, G.J., Boutet, S., Messinger, J., Zouni, A., Yano, J., Bergmann, U., Yachandra, V.K., Adams, P.D., Sauter, N.K.

(2014) Nat Methods 11: 545-548

• PubMed: 24633409 
• DOI: https://doi.org/10.1038/nmeth.2887
• Primary Citation Related Structures: 
  4OW3


• PubMed Abstract: 
  

  X-ray free-electron laser (XFEL) sources enable the use of crystallography to solve three-dimensional macromolecular structures under native conditions and without radiation damage. Results to date, however, have been limited by the challenge of deriving accurate Bragg intensities from a heterogeneous population of microcrystals, while at the same time modeling the X-ray spectrum and detector geometry. Here we present a computational approach designed to extract meaningful high-resolution signals from fewer diffraction measurements.

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Organizational Affiliation: 
• Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
1] Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA. [2].
Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California, USA.
Max-Volmer-Laboratorium für Biophysikalische Chemie, Technische Universität, Berlin, Germany.
Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, California, USA.
Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California, USA.
1] Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California, USA. [2] Department of Physics, AlbaNova, Stockholm University, Stockholm, Sweden.
European Synchrotron Radiation Facility, Grenoble, France.
1] Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California, USA. [2] Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, California, USA.
Institutionen för Kemi, Kemiskt Biologiskt Centrum, Umeå Universitet, Umeå, Sweden.
1] Max-Volmer-Laboratorium für Biophysikalische Chemie, Technische Universität, Berlin, Germany. [2] Institut für Biologie, Humboldt Universität zu Berlin, Berlin, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 34.59 kDa 
• Atom Count: 2,747 
• Modeled Residue Count: 314 
• Deposited Residue Count: 316 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thermolysin	A	316	Bacillus thermoproteolyticus	Mutation(s): 0  EC: 3.4.24.27
UniProt
Find proteins for P00800 (Bacillus thermoproteolyticus) Explore P00800  Go to UniProtKB:  P00800

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	C [auth A], D [auth A], E [auth A], F [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.263 (Depositor), 0.267 (DCC) 
• R-Value Work:  0.217 (Depositor), 0.225 (DCC) 
• R-Value Observed: 0.220 (Depositor) 

Diffraction Data: https://doi.org/10.11577/1169543

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.8933	α = 90
b = 92.8933	β = 90
c = 130.438	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2014-03-12 
Deposition Author(s): Hattne, J., Echols, N., Tran, R., Kern, J., Gildea, R.J., Brewster, A.S., Alonso-Mori, R., Glockner, C., Hellmich, J., Laksmono, H., Sierra, R.G., Lassalle-Kaiser, B., Lampe, A., Han, G., Gul, S., DiFiore, D., Milathianaki, D., Fry, A.R., Miahnahri, A., White, W.E., Schafer, D.W., Seibert, M.M., Koglin, J.E., Sokaras, D., Weng, T.-C., Sellberg, J., Latimer, M.J., Glatzel, P., Zwart, P.H., Grosse-Kunstleve, R.W., Bogan, M.J., Messerschmidt, M., Williams, G.J., Boutet, S., Messinger, J., Zouni, A., Yano, J., Bergmann, U., Yachandra, V.K., Adams, P.D., Sauter, N.K.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM095887
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM102520
Department of Energy (DOE, United States)	United States	DE-AC02-05CH11231
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM055302
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P41GM103393

Revision History  

• Version 1.0: 2014-03-12
  Type: Initial release
  
• Version 1.1: 2014-06-18
  Changes: Database references
• Version 1.2: 2015-02-04
  Changes: Derived calculations
• Version 1.3: 2017-09-27
  Changes: Advisory, Author supporting evidence, Database references, Derived calculations, Other, Source and taxonomy, Structure summary
• Version 1.4: 2019-12-04
  Changes: Author supporting evidence
• Version 1.5: 2023-08-16
  Changes: Data collection, Database references, Refinement description
• Version 1.6: 2023-09-27
  Changes: Refinement description