HEADER PROTEIN BINDING 05-APR-24 9BB2 TITLE BACKBONE MODIFICATION IN THE GA MODULE OF PROTEIN PAB: BETA3-RESIDUES TITLE 2 AT POSITIONS 20 AND 24 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTOSTREPTOCOCCAL ALBUMIN-BINDING PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: FINEGOLDIA MAGNA; SOURCE 4 ORGANISM_TAXID: 1260 KEYWDS HELIX BUNDLE, DESIGNED VARIANT, PROTEIN BINDING EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR Y.LIN,W.S.HORNE REVDAT 1 05-JUN-24 9BB2 0 JRNL AUTH Y.LIN,W.S.HORNE JRNL TITL BACKBONE MODIFICATION IN A PROTEIN HYDROPHOBIC CORE. JRNL REF CHEMISTRY 01890 2024 JRNL REFN ISSN 0947-6539 JRNL PMID 38753977 JRNL DOI 10.1002/CHEM.202401890 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : ARIA REMARK 3 AUTHORS : LINGE, O'DONOGHUE AND NILGES REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 9BB2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-APR-24. REMARK 100 THE DEPOSITION ID IS D_1000282983. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 283 REMARK 210 PH : 6 REMARK 210 IONIC STRENGTH : 1 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1 MM GA MODULE OF PROTEIN PAB: REMARK 210 BETA3 RESIDUES AT POSITIONS 20 REMARK 210 AND 24, 0.2 MM DSS, 90% H2O/10% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H TOCSY; 2D 1H-1H COSY; REMARK 210 2D 1H-1H NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN, POKY, ARIA REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 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 1 B3D A 20 CA - C - N ANGL. DEV. = 14.4 DEGREES REMARK 500 2 B3D A 20 CA - C - N ANGL. DEV. = 14.8 DEGREES REMARK 500 4 B3D A 20 CA - C - N ANGL. DEV. = 14.4 DEGREES REMARK 500 5 B3D A 20 CA - C - N ANGL. DEV. = 15.8 DEGREES REMARK 500 7 B3D A 20 CA - C - N ANGL. DEV. = 15.7 DEGREES REMARK 500 8 B3D A 20 CA - C - N ANGL. DEV. = 17.8 DEGREES REMARK 500 9 B3D A 20 CA - C - N ANGL. DEV. = 17.7 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 3 THR A 18 45.87 -106.90 REMARK 500 4 LYS A 2 -71.99 -71.18 REMARK 500 4 THR A 18 62.10 -118.70 REMARK 500 4 B3D A 20 -9.87 -53.17 REMARK 500 5 ASN A 3 20.28 -157.91 REMARK 500 5 THR A 18 44.28 -103.88 REMARK 500 6 LYS A 2 -65.97 -103.62 REMARK 500 6 ASN A 3 23.51 -148.45 REMARK 500 6 THR A 18 56.76 -105.59 REMARK 500 7 THR A 18 49.15 -104.37 REMARK 500 8 THR A 18 54.56 -100.22 REMARK 500 8 B3D A 20 -8.59 -59.31 REMARK 500 9 LYS A 2 -60.96 -153.09 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 B3D A 20 PHE A 21 1 149.97 REMARK 500 B3X A 24 ALA A 25 1 146.20 REMARK 500 B3X A 24 ALA A 25 2 147.53 REMARK 500 B3D A 20 PHE A 21 3 148.07 REMARK 500 B3X A 24 ALA A 25 3 146.36 REMARK 500 B3X A 24 ALA A 25 4 146.22 REMARK 500 B3X A 24 ALA A 25 5 147.26 REMARK 500 B3D A 20 PHE A 21 6 148.94 REMARK 500 B3X A 24 ALA A 25 6 147.32 REMARK 500 B3X A 24 ALA A 25 7 147.31 REMARK 500 B3X A 24 ALA A 25 8 146.57 REMARK 500 B3X A 24 ALA A 25 9 147.29 REMARK 500 B3D A 20 PHE A 21 10 149.66 REMARK 500 B3X A 24 ALA A 25 10 147.78 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 1 B3D A 20 -19.30 REMARK 500 1 B3X A 24 -19.26 REMARK 500 2 B3D A 20 -18.33 REMARK 500 2 B3X A 24 -19.39 REMARK 500 3 B3D A 20 -19.45 REMARK 500 3 B3X A 24 -18.55 REMARK 500 4 B3D A 20 -18.62 REMARK 500 4 B3X A 24 -18.57 REMARK 500 5 B3D A 20 -19.40 REMARK 500 5 B3X A 24 -18.69 REMARK 500 6 B3D A 20 -19.45 REMARK 500 6 B3X A 24 -18.80 REMARK 500 7 B3D A 20 -18.86 REMARK 500 7 B3X A 24 -18.55 REMARK 500 8 B3D A 20 -17.96 REMARK 500 8 B3X A 24 -18.60 REMARK 500 9 B3D A 20 -18.16 REMARK 500 9 B3X A 24 -18.91 REMARK 500 10 B3D A 20 -19.16 REMARK 500 10 B3X A 24 -18.80 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 31158 RELATED DB: BMRB REMARK 900 BACKBONE MODIFICATION IN THE GA MODULE OF PROTEIN PAB: BETA3- REMARK 900 RESIDUES AT POSITIONS 20 AND 24 DBREF 9BB2 A 1 47 UNP Q51911 PAB_FINMA 219 265 SEQADV 9BB2 NH2 A 48 UNP Q51911 AMIDATION SEQRES 1 A 48 LEU LYS ASN ALA LYS GLU ASP ALA ILE ALA GLU LEU LYS SEQRES 2 A 48 LYS ALA GLY ILE THR SER B3D PHE TYR PHE B3X ALA ILE SEQRES 3 A 48 ASN LYS ALA LYS THR VAL GLU GLU VAL ASN ALA LEU LYS SEQRES 4 A 48 ASN GLU ILE LEU LYS ALA HIS ALA NH2 MODRES 9BB2 B3D A 20 ASP MODIFIED RESIDUE MODRES 9BB2 B3X A 24 ASN MODIFIED RESIDUE HET B3D A 20 15 HET B3X A 24 17 HET NH2 A 48 3 HETNAM B3D 3-AMINOPENTANEDIOIC ACID HETNAM B3X (3S)-3,5-DIAMINO-5-OXOPENTANOIC ACID HETNAM NH2 AMINO GROUP HETSYN B3D BETA-HOMOASPARTATE FORMUL 1 B3D C5 H9 N O4 FORMUL 1 B3X C5 H10 N2 O3 FORMUL 1 NH2 H2 N HELIX 1 AA1 LEU A 1 GLY A 16 1 16 HELIX 2 AA2 SER A 19 ALA A 29 1 11 HELIX 3 AA3 THR A 31 ALA A 47 1 17 LINK C SER A 19 N B3D A 20 1555 1555 1.33 LINK C B3D A 20 N PHE A 21 1555 1555 1.33 LINK C PHE A 23 N B3X A 24 1555 1555 1.33 LINK C B3X A 24 N ALA A 25 1555 1555 1.34 LINK C ALA A 47 N NH2 A 48 1555 1555 1.32 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 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 MODEL 1