HEADER BLOOD CLOTTING 18-AUG-23 8TVL TITLE PLASMINOGEN BINDING GROUP A STREPTOCOCCUS M-LIKE PROTEIN FROM AP53 TITLE 2 BOUND TO HUMAN PLASMINOGEN COMPND MOL_ID: 1; COMPND 2 MOLECULE: M PROTEIN (FRAGMENT); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOCOCCUS PYOGENES; SOURCE 3 ORGANISM_TAXID: 1314; SOURCE 4 STRAIN: AP53; SOURCE 5 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 7 EXPRESSION_SYSTEM_CELL_LINE: HEK293T KEYWDS PAM, HUMAN PLASMINOGEN, M-PROTEIN, GROUP A STREPTOCOCCUS, BLOOD KEYWDS 2 CLOTTING EXPDTA ELECTRON MICROSCOPY AUTHOR B.M.READNOUR,S.K.TJIA-FLECK,F.J.CASTELLINO,N.R.MCCANN REVDAT 2 13-DEC-23 8TVL 1 REMARK REVDAT 1 11-OCT-23 8TVL 0 JRNL AUTH B.M.READNOUR,S.K.TJIA-FLECK,N.R.MCCANN,Y.A.AYINUOLA, JRNL AUTH 2 V.A.PLOPLIS,F.J.CASTELLINO JRNL TITL PLASMINOGEN BINDING GROUP A STREPTOCOCCUS M-LIKE PROTEIN JRNL TITL 2 FROM AP53 BOUND TO HUMAN PLASMINOGEN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : UCSF CHIMERAX, CRYOSPARC, PHENIX REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : RIGID BODY FIT REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : NULL REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 3.800 REMARK 3 NUMBER OF PARTICLES : 212829 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING AND AMPLITUDE REMARK 3 CORRECTION REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 8TVL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-AUG-23. REMARK 100 THE DEPOSITION ID IS D_1000276743. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : SINGLE PARTICLE REMARK 245 SPECIMEN TYPE : NULL REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : PARTICLE REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : PLASMINOGEN BINDING GROUP A REMARK 245 STREPTOCOCCUS M-LIKE PROTEIN REMARK 245 FROM AP53 BOUND TO HUMAN REMARK 245 PLASMINOGEN REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.40 REMARK 245 SAMPLE DETAILS : PAM WAS BOUND TO THE SURFACE OF REMARK 245 A LENTIVIRUS REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : 4054 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : TFS KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1000.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 34000.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : 2.70 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 5500.00 REMARK 245 ILLUMINATION MODE : SPOT SCAN REMARK 245 NOMINAL MAGNIFICATION : 109000 REMARK 245 CALIBRATED MAGNIFICATION : NULL REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 300 REMARK 245 IMAGING DETAILS : NULL REMARK 247 REMARK 247 ELECTRON MICROSCOPY REMARK 247 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM ELECTRON REMARK 247 MICROSCOPY DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE REMARK 247 THAT CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES REMARK 247 ON THESE RECORDS ARE MEANINGLESS EXCEPT FOR THE CALCULATION REMARK 247 OF THE STRUCTURE FACTORS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 ASN A 1 REMARK 465 ARG A 2 REMARK 465 ALA A 3 REMARK 465 ASP A 4 REMARK 465 ASP A 5 REMARK 465 ALA A 6 REMARK 465 ARG A 7 REMARK 465 ASN A 8 REMARK 465 GLU A 9 REMARK 465 VAL A 10 REMARK 465 LEU A 11 REMARK 465 ARG A 12 REMARK 465 GLY A 13 REMARK 465 ASN A 14 REMARK 465 LEU A 15 REMARK 465 VAL A 16 REMARK 465 ARG A 17 REMARK 465 ALA A 18 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 C GLN A 130 H LYS A 131 1.14 REMARK 500 O GLU A 219 H ILE A 223 1.53 REMARK 500 O ALA A 195 HH11 ARG A 233 1.55 REMARK 500 O ALA A 318 H ASN A 322 1.59 REMARK 500 O SER A 313 H ASP A 317 1.60 REMARK 500 O LEU A 302 OG SER A 311 1.97 REMARK 500 O GLU A 219 N ILE A 223 2.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 LYS A 53 O - C - N ANGL. DEV. = -18.8 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ILE A 25 -70.55 -122.22 REMARK 500 LEU A 33 130.28 -35.90 REMARK 500 LEU A 42 45.84 -90.08 REMARK 500 GLU A 44 -106.02 68.75 REMARK 500 GLU A 47 -162.48 -78.04 REMARK 500 GLU A 48 66.07 -69.14 REMARK 500 LYS A 53 -149.49 34.14 REMARK 500 GLU A 57 -168.43 -128.78 REMARK 500 ALA A 61 -7.78 78.21 REMARK 500 GLU A 64 -178.52 -65.42 REMARK 500 LEU A 68 -162.47 -78.47 REMARK 500 GLU A 74 37.68 -98.48 REMARK 500 GLU A 77 92.28 -68.72 REMARK 500 ARG A 80 30.71 -96.75 REMARK 500 HIS A 88 76.27 -105.99 REMARK 500 ASP A 89 3.81 -64.99 REMARK 500 LYS A 91 -125.78 50.08 REMARK 500 ARG A 95 -60.20 -90.50 REMARK 500 LYS A 101 -134.56 59.40 REMARK 500 ALA A 103 -95.06 59.93 REMARK 500 ASP A 104 -115.08 52.60 REMARK 500 GLN A 106 133.99 -170.22 REMARK 500 GLU A 107 -94.83 57.59 REMARK 500 ALA A 112 -9.91 74.14 REMARK 500 LEU A 113 147.94 57.44 REMARK 500 LYS A 119 31.06 -140.88 REMARK 500 GLU A 129 2.51 -67.19 REMARK 500 LYS A 174 25.92 49.58 REMARK 500 ASP A 194 -62.87 -109.78 REMARK 500 ASN A 209 72.72 -69.07 REMARK 500 THR A 211 50.14 -90.11 REMARK 500 ALA A 212 7.06 59.08 REMARK 500 GLU A 213 -157.41 33.02 REMARK 500 ASP A 215 159.73 179.96 REMARK 500 LYS A 216 173.44 58.99 REMARK 500 ALA A 252 -19.17 -49.77 REMARK 500 GLU A 260 170.00 -57.62 REMARK 500 LYS A 261 -6.96 80.01 REMARK 500 GLU A 276 -136.17 58.92 REMARK 500 GLU A 300 -60.96 -95.95 REMARK 500 ARG A 306 -163.57 -75.92 REMARK 500 ALA A 307 65.95 65.24 REMARK 500 GLU A 308 67.71 63.17 REMARK 500 LYS A 309 128.44 -37.06 REMARK 500 ALA A 324 30.14 70.04 REMARK 500 LYS A 342 88.73 -150.07 REMARK 500 GLU A 347 129.76 -38.13 REMARK 500 LYS A 349 -62.38 -91.38 REMARK 500 LEU A 352 74.70 49.06 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 SER A 196 ARG A 197 146.78 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 LYS A 53 27.60 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-42429 RELATED DB: EMDB DBREF 8TVL A 1 356 UNP Q6V4L8 Q6V4L8_STRPY 30 385 SEQRES 1 A 356 ASN ARG ALA ASP ASP ALA ARG ASN GLU VAL LEU ARG GLY SEQRES 2 A 356 ASN LEU VAL ARG ALA GLU LEU TRP TYR ARG GLN ILE GLN SEQRES 3 A 356 GLU ASN ASP GLN LEU LYS LEU GLU ASN LYS GLY LEU LYS SEQRES 4 A 356 THR ASP LEU ARG GLU LYS GLU GLU GLU LEU GLN GLY LEU SEQRES 5 A 356 LYS ASP ASP VAL GLU LYS LEU THR ALA ASP ALA GLU LEU SEQRES 6 A 356 GLN ARG LEU LYS ASN GLU ARG HIS GLU GLU ALA GLU LEU SEQRES 7 A 356 GLU ARG LEU LYS SER GLU ARG HIS ASP HIS ASP LYS LYS SEQRES 8 A 356 GLU ALA GLU ARG LYS ALA LEU GLU ASP LYS LEU ALA ASP SEQRES 9 A 356 LYS GLN GLU HIS LEU ASN GLY ALA LEU ARG TYR ILE ASN SEQRES 10 A 356 GLU LYS GLU ALA GLU ARG LYS GLU LYS GLU ALA GLU GLN SEQRES 11 A 356 LYS LYS LEU LYS GLU GLU LYS GLN ILE SER ASP ALA SER SEQRES 12 A 356 ARG GLN GLY LEU ARG ARG ASP LEU ASP ALA SER ARG GLU SEQRES 13 A 356 ALA LYS LYS GLN VAL GLU LYS ASP LEU ALA ASN LEU THR SEQRES 14 A 356 ALA GLU LEU ASP LYS VAL LYS GLU GLU LYS GLN ILE SER SEQRES 15 A 356 ASP ALA SER ARG GLN GLY LEU ARG ARG ASP LEU ASP ALA SEQRES 16 A 356 SER ARG GLU ALA LYS LYS GLN VAL GLU LYS GLY LEU ALA SEQRES 17 A 356 ASN LEU THR ALA GLU LEU ASP LYS VAL LYS GLU GLU LYS SEQRES 18 A 356 GLN ILE SER ASP ALA SER ARG GLN GLY LEU ARG ARG ASP SEQRES 19 A 356 LEU ASP ALA SER ARG GLU ALA LYS LYS GLN VAL GLU LYS SEQRES 20 A 356 ALA LEU GLU GLU ALA ASN SER LYS LEU ALA ALA LEU GLU SEQRES 21 A 356 LYS LEU ASN LYS GLU LEU GLU GLU SER LYS LYS LEU THR SEQRES 22 A 356 GLU LYS GLU LYS ALA GLU LEU GLN ALA LYS LEU GLU ALA SEQRES 23 A 356 GLU ALA LYS ALA LEU LYS GLU GLN LEU ALA LYS GLN ALA SEQRES 24 A 356 GLU GLU LEU ALA LYS LEU ARG ALA GLU LYS ALA SER ASP SEQRES 25 A 356 SER GLN THR PRO ASP ALA LYS PRO GLY ASN LYS ALA VAL SEQRES 26 A 356 PRO GLY LYS GLY GLN ALA PRO GLN ALA GLY THR LYS PRO SEQRES 27 A 356 ASN GLN ASN LYS ALA PRO MET LYS GLU THR LYS ARG GLN SEQRES 28 A 356 LEU PRO SER THR GLY HELIX 1 AA1 LEU A 133 LEU A 151 1 19 HELIX 2 AA2 LEU A 151 ALA A 157 1 7 HELIX 3 AA3 GLU A 177 SER A 196 1 20 HELIX 4 AA4 SER A 196 ALA A 208 1 13 HELIX 5 AA5 LYS A 218 ALA A 241 1 24 HELIX 6 AA6 LEU A 256 GLU A 260 5 5 HELIX 7 AA7 ASN A 263 GLU A 268 1 6 HELIX 8 AA8 ALA A 278 ALA A 290 1 13 HELIX 9 AA9 ALA A 290 ALA A 299 1 10 HELIX 10 AB1 SER A 313 LYS A 323 1 11 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000