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- PDB-9tro: Factor VII Gla domain, X-ray structure -

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Basic information

Entry
Database: PDB / ID: 9tro
TitleFactor VII Gla domain, X-ray structure
ComponentsFactor VII light chain
KeywordsPROTEIN BINDING / Factor VIIa / coagulation / hemophilia / bleeding / EPCR / complex
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsLopez-Sagaseta, J.
Funding support Spain, 2items
OrganizationGrant numberCountry
Ministerio de Ciencia e Innovacion (MCIN)RYC201721683 Spain
Ministerio de Ciencia e Innovacion (MCIN)PID2022-139888NB-I00 Spain
CitationJournal: Blood Adv / Year: 2026
Title: Structure of Factor VII Gla domain bound to EPCR.
Authors: Lopez-Sagaseta, J. / Dichiara-Rodriguez, M.G.
History
DepositionDec 25, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 25, 2026Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2026Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: Factor VII light chain
A: Factor VII light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,96517
Polymers8,3812
Non-polymers58415
Water1,47782
1
L: Factor VII light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,4718
Polymers4,1901
Non-polymers2817
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Factor VII light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,4949
Polymers4,1901
Non-polymers3048
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)24.470, 29.673, 33.259
Angle α, β, γ (deg.)88.335, 78.611, 76.921
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11L
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: ILE / End label comp-ID: ILE / Auth seq-ID: 1 - 30 / Label seq-ID: 1 - 30

Dom-IDAuth asym-IDLabel asym-ID
1LA
2AB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein/peptide Factor VII light chain


Mass: 4190.295 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: CHEMICALLY SYNTHESIZED PEPTIDE WITH DISULFIDE BRIDGE
Source: (synth.) Homo sapiens (human)
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.75 Å3/Da / Density % sol: 55.29 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 2.0 M Malonate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XAIRA / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Oct 3, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.55→32.6 Å / Num. obs: 12546 / % possible obs: 96.8 % / Redundancy: 3.3 % / Biso Wilson estimate: 10.26 Å2 / CC1/2: 0.928 / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.083 / Rrim(I) all: 0.151 / Χ2: 0.69 / Net I/σ(I): 3.8
Reflection shellResolution: 1.55→1.58 Å / Rmerge(I) obs: 0.521 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 607 / CC1/2: 0.832 / Rpim(I) all: 0.343 / Rrim(I) all: 0.626 / Χ2: 1.28

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Processing

Software
NameVersionClassification
REFMAC5.8.0431refinement
XDSJan 19, 2025data reduction
Aimless1.14.2data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→32.6 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.961 / WRfactor Rfree: 0.215 / WRfactor Rwork: 0.176 / SU B: 3.52 / SU ML: 0.056 / Average fsc free: 0.9795 / Average fsc work: 0.9875 / Cross valid method: THROUGHOUT / ESU R: 0.082 / ESU R Free: 0.065
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.1707 636 5.069 %RANDOM
Rwork0.1519 11910 --
all0.153 ---
obs-12546 96.806 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 14.42 Å2
Baniso -1Baniso -2Baniso -3
1--0.214 Å20.859 Å20.186 Å2
2---1.158 Å20.746 Å2
3---1.731 Å2
Refinement stepCycle: LAST / Resolution: 1.55→32.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms557 0 15 82 654
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.013581
X-RAY DIFFRACTIONr_bond_other_d0.0010.016452
X-RAY DIFFRACTIONr_angle_refined_deg1.7721.803795
X-RAY DIFFRACTIONr_angle_other_deg0.6931.6911051
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.778564
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3.67556
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.2091057
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.1521015
X-RAY DIFFRACTIONr_chiral_restr0.1060.290
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02714
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02130
X-RAY DIFFRACTIONr_nbd_refined0.2810.2221
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1960.2430
X-RAY DIFFRACTIONr_nbtor_refined0.1760.2283
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.2274
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2460.239
X-RAY DIFFRACTIONr_metal_ion_refined0.0950.258
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.4630.211
X-RAY DIFFRACTIONr_nbd_other0.1720.27
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2090.24
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1560.24
X-RAY DIFFRACTIONr_mcbond_it3.8571.518256
X-RAY DIFFRACTIONr_mcbond_other3.851.515255
X-RAY DIFFRACTIONr_mcangle_it5.6932.728317
X-RAY DIFFRACTIONr_mcangle_other5.6912.73318
X-RAY DIFFRACTIONr_scbond_it4.2871.676325
X-RAY DIFFRACTIONr_scbond_other4.2811.677326
X-RAY DIFFRACTIONr_scangle_it6.2663.02477
X-RAY DIFFRACTIONr_scangle_other6.2593.02478
X-RAY DIFFRACTIONr_lrange_it12.81218.877784
X-RAY DIFFRACTIONr_lrange_other11.23517.714750
X-RAY DIFFRACTIONr_rigid_bond_restr3.63931033
X-RAY DIFFRACTIONr_ncsr_local_group_10.0310.051131
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11LX-RAY DIFFRACTIONLocal ncs0.031140.05009
12AX-RAY DIFFRACTIONLocal ncs0.031140.05009
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.55-1.590.32430.2098440.2149290.930.97895.4790.213
1.59-1.6340.206390.178780.1729710.9770.98794.43870.179
1.634-1.6810.237430.1488110.1528910.980.98995.84740.16
1.681-1.7330.151390.1198120.1218950.9820.99395.08380.131
1.733-1.7890.159540.1117600.1158460.9830.99496.21750.126
1.789-1.8520.135380.1067760.1078480.9890.99495.99060.12
1.852-1.9220.125380.1096930.117550.9910.99496.82120.124
1.922-20.154460.1177110.1197840.9870.99396.55610.139
2-2.0880.151290.1186870.1197370.9820.99297.15060.138
2.088-2.190.183290.1326520.1347030.9810.9996.87060.159
2.19-2.3080.163390.1246160.1276680.9810.99298.05390.161
2.308-2.4470.14300.1315960.1316420.9870.9997.50780.166
2.447-2.6150.166330.1395370.145840.9840.98997.60270.18
2.615-2.8230.184250.1645310.1655640.9770.98698.58160.214
2.823-3.090.196330.1744710.1755130.9790.98198.24560.228
3.09-3.4510.121180.164300.1584560.9930.98498.24560.205
3.451-3.9770.174200.1743750.1743990.9840.98298.99750.219
3.977-4.8530.176210.1633290.1643530.9830.98499.15010.219
4.853-6.7880.223170.2152460.2162640.9720.97699.62120.306
6.788-32.60.03320.281540.2771570.9990.999.36310.505

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