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- PDB-5mhl: FXIIIa in complex with the inhibitor Mi0621 -

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Basic information

Entry
Database: PDB / ID: 5mhl
TitleFXIIIa in complex with the inhibitor Mi0621
Components
  • Coagulation factor XIII A chain
  • inhibitor Mi0621
KeywordsTRANSFERASE / factor XIII / inhibition / transglutaminase
Function / homology
Function and homology information


protein-glutamine gamma-glutamyltransferase / protein-glutamine gamma-glutamyltransferase activity / transferase complex / peptide cross-linking / blood coagulation, fibrin clot formation / Common Pathway of Fibrin Clot Formation / platelet alpha granule lumen / blood coagulation / Platelet degranulation / Interleukin-4 and Interleukin-13 signaling ...protein-glutamine gamma-glutamyltransferase / protein-glutamine gamma-glutamyltransferase activity / transferase complex / peptide cross-linking / blood coagulation, fibrin clot formation / Common Pathway of Fibrin Clot Formation / platelet alpha granule lumen / blood coagulation / Platelet degranulation / Interleukin-4 and Interleukin-13 signaling / collagen-containing extracellular matrix / blood microparticle / extracellular space / extracellular region / metal ion binding
Similarity search - Function
Coagulation Factor XIII; Chain A, domain 2 / Transglutaminase-like / : / Transglutaminase, N-terminal / Transglutaminase, C-terminal / Transglutaminase, active site / Protein-glutamine gamma-glutamyltransferase, animal / Transglutaminase, C-terminal domain superfamily / Transglutaminase family / Transglutaminase family, C-terminal ig like domain ...Coagulation Factor XIII; Chain A, domain 2 / Transglutaminase-like / : / Transglutaminase, N-terminal / Transglutaminase, C-terminal / Transglutaminase, active site / Protein-glutamine gamma-glutamyltransferase, animal / Transglutaminase, C-terminal domain superfamily / Transglutaminase family / Transglutaminase family, C-terminal ig like domain / Transglutaminases active site. / Transglutaminase-like superfamily / Transglutaminase/protease-like homologues / Transglutaminase-like / Transglutaminase-like superfamily / Papain-like cysteine peptidase superfamily / Immunoglobulin E-set / Immunoglobulins / Immunoglobulin-like fold / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Coagulation factor XIII A chain
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å
AuthorsStieler, M. / Heine, A. / Klebe, G.
Funding support Germany, 1items
OrganizationGrant numberCountry
BMBFFKZ0316030 Germany
Citation
Journal: To Be Published
Title: FXIIIa in complex with the inhibitor Mi0621
Authors: Stieler, M. / Heine, A. / Klebe, G.
#1: Journal: Angew Chem Int Ed Engl. / Year: 2013
Title: Structure of active coagulation factor XIII triggered by calcium binding: basis for the design of next-generation anticoagulants.
Authors: Stieler, M. / Weber, J. / Hils, M. / Kolb, P. / Heine, A. / Buechold, C. / Pasternack, R. / Klebe, G.
History
DepositionNov 24, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Coagulation factor XIII A chain
B: Coagulation factor XIII A chain
K: inhibitor Mi0621
O: inhibitor Mi0621
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,41620
Polymers170,2684
Non-polymers1,14716
Water6,630368
1
A: Coagulation factor XIII A chain
K: inhibitor Mi0621
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,78511
Polymers85,1342
Non-polymers6519
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Coagulation factor XIII A chain
O: inhibitor Mi0621
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,6319
Polymers85,1342
Non-polymers4977
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.213, 80.993, 103.329
Angle α, β, γ (deg.)88.12, 76.87, 81.47
Int Tables number1
Space group name H-MP1

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABKO

#1: Protein Coagulation factor XIII A chain / Coagulation factor XIIIa / Protein-glutamine gamma-glutamyltransferase A chain / Transglutaminase A chain


Mass: 84206.039 Da / Num. of mol.: 2 / Mutation: T649I, Q651E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F13A1, F13A / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P00488, protein-glutamine gamma-glutamyltransferase
#2: Protein/peptide inhibitor Mi0621


Mass: 928.168 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 384 molecules

#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 368 / 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: 2.73 Å3/Da / Density % sol: 54.87 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 170 mM ammonium sulfate, 85 mM sodium cacodylate, 25.5 % PEG8000, 15 % glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97779 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97779 Å / Relative weight: 1
ReflectionResolution: 2.4→48.83 Å / Num. obs: 65090 / % possible obs: 92.6 % / Observed criterion σ(I): -3 / Redundancy: 2 % / Rsym value: 0.087 / Net I/σ(I): 7.36
Reflection shellResolution: 2.4→2.54 Å / Redundancy: 2 % / Rmerge(I) obs: 0.352 / Mean I/σ(I) obs: 2 / % possible all: 87.7

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
Cootmodel building
RefinementResolution: 2.4→48.83 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 27.56
RfactorNum. reflection% reflectionSelection details
Rfree0.2305 3254 5 %Random selection
Rwork0.1717 ---
obs0.1747 65031 92.53 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.4→48.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10819 0 119 368 11306
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00911231
X-RAY DIFFRACTIONf_angle_d1.41615237
X-RAY DIFFRACTIONf_dihedral_angle_d13.1846523
X-RAY DIFFRACTIONf_chiral_restr0.0581692
X-RAY DIFFRACTIONf_plane_restr0.0061966
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.395-2.43080.31581180.25292229X-RAY DIFFRACTION78
2.4308-2.46880.32751420.24732713X-RAY DIFFRACTION92
2.4688-2.50930.37911390.2382622X-RAY DIFFRACTION91
2.5093-2.55250.28711360.23282593X-RAY DIFFRACTION90
2.5525-2.59890.32391400.22252653X-RAY DIFFRACTION89
2.5989-2.64890.26541390.21522635X-RAY DIFFRACTION92
2.6489-2.7030.34081430.22662732X-RAY DIFFRACTION93
2.703-2.76170.3411390.22072628X-RAY DIFFRACTION92
2.7617-2.8260.32751420.21922707X-RAY DIFFRACTION93
2.826-2.89660.25641410.21222691X-RAY DIFFRACTION92
2.8966-2.9750.28461400.2132666X-RAY DIFFRACTION92
2.975-3.06250.27221430.19442702X-RAY DIFFRACTION94
3.0625-3.16130.25761450.18942760X-RAY DIFFRACTION94
3.1613-3.27430.23511400.18492662X-RAY DIFFRACTION93
3.2743-3.40530.22361430.17322724X-RAY DIFFRACTION92
3.4053-3.56030.23041470.17012786X-RAY DIFFRACTION96
3.5603-3.74790.19791440.15052743X-RAY DIFFRACTION96
3.7479-3.98260.20841470.13792793X-RAY DIFFRACTION96
3.9826-4.290.1711470.12472786X-RAY DIFFRACTION95
4.29-4.72140.15481450.11752758X-RAY DIFFRACTION95
4.7214-5.40380.16941450.12532744X-RAY DIFFRACTION94
5.4038-6.80530.20691450.16332765X-RAY DIFFRACTION96
6.8053-48.8430.19321440.16842685X-RAY DIFFRACTION92
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)
10.50020.05050.9134-0.1894-0.15683.12720.10410.0044-0.0212-0.0797-0.04890.15320.0871-0.0336-0.0630.287-0.0091-0.03930.1941-0.01660.333631.751258.916-30.46
20.83840.03650.69351.89471.13491.4384-0.0467-0.12540.0390.12910.0142-0.0591-0.0107-0.12280.02150.2789-0.0244-0.01510.2452-0.00150.248945.147369.626-3.7009
31.30840.3250.4831.56070.3081.62370.0226-0.1339-0.04370.39850.053-0.41130.13270.1916-0.09660.3881-0.0119-0.11960.2658-0.00390.37760.074659.48483.3945
43.4476-1.3123-0.29060.56550.04940.7207-0.2004-0.23530.04060.24780.0589-0.3386-0.11020.21190.1140.4366-0.0186-0.15550.32370.01110.505567.4835.8059-1.3761
53.34250.47311.91225.3694-0.1075.087-0.39250.4646-0.2903-0.27090.6529-0.185-0.1772-0.1508-0.21010.3108-0.0147-0.03310.38930.02760.288238.871915.5129-12.6136
60.4717-0.1540.72040.0189-0.29783.51840.06770.0279-0.0583-0.0583-0.01490.11650.1215-0.2002-0.05540.2359-0.0272-0.03350.20380.00070.304637.536519.573819.1471
70.5505-0.18020.13510.7920.0890.7427-0.0515-0.12550.03270.12340.0158-0.09780.05080.01810.03520.2893-0.0198-0.02940.24770.00990.287758.942221.889251.3744
84.08920.56470.90280.27720.69690.41290.0706-0.1802-0.18590.1051-0.0288-0.11320.09890.0249-0.03980.3252-0.0166-0.03470.27120.06140.373771.507-6.686848.8407
97.9375-1.31271.63933.5556-1.19372.4530.3390.3829-0.4428-0.291-0.09640.15590.1335-0.2348-0.21840.37-0.0064-0.01810.2579-0.01510.304843.7901-26.671235.0745
107.2060.83333.56361.71331.36014.0122-0.1262-0.0899-0.20870.00670.34870.3414-0.5269-0.4858-0.29220.37070.0513-0.03450.32670.13850.430236.4384-20.282236.2739
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 15:192)
2X-RAY DIFFRACTION2(chain A and resid 193:318)
3X-RAY DIFFRACTION3(chain A and resid 319:497)
4X-RAY DIFFRACTION4(chain A and resid 498:628)
5X-RAY DIFFRACTION5(chain A and resid 629:726)
6X-RAY DIFFRACTION6(chain B and resid 15:189)
7X-RAY DIFFRACTION7(chain B and resid 190:516)
8X-RAY DIFFRACTION8(chain B and resid 517:629)
9X-RAY DIFFRACTION9(chain B and resid 630:691)
10X-RAY DIFFRACTION10(chain B and resid 692:730)

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