HEADER PLANT DEFENSIN 15-JUL-98 1BK8 TITLE DETERMINATION OF THE THREE-DIMENSIONAL SOLUTION STRUCTURE OF AESCULUS TITLE 2 HIPPOCASTANUM ANTIMICROBIAL PROTEIN 1 (AH-AMP1) BY 1H NMR, 25 TITLE 3 STRUCTURES COMPND MOL_ID: 1; COMPND 2 MOLECULE: ANTIMICROBIAL PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: AH-AMP1 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AESCULUS HIPPOCASTANUM; SOURCE 3 ORGANISM_COMMON: COMMON HORSE CHESTNUT; SOURCE 4 ORGANISM_TAXID: 43364; SOURCE 5 ORGAN: SEED KEYWDS PLANT DEFENSIN, ANTIMICROBIAL, CYSTEINE-STABILIZED ALFA/ BETA MOTIF EXPDTA SOLUTION NMR NUMMDL 25 AUTHOR F.FANT,F.A.M.BORREMANS REVDAT 4 29-NOV-17 1BK8 1 REMARK HELIX REVDAT 3 24-FEB-09 1BK8 1 VERSN REVDAT 2 01-APR-03 1BK8 1 JRNL REVDAT 1 05-JAN-00 1BK8 0 JRNL AUTH F.FANT,W.F.VRANKEN,F.A.BORREMANS JRNL TITL THE THREE-DIMENSIONAL SOLUTION STRUCTURE OF AESCULUS JRNL TITL 2 HIPPOCASTANUM ANTIMICROBIAL PROTEIN 1 DETERMINED BY 1H JRNL TITL 3 NUCLEAR MAGNETIC RESONANCE. JRNL REF PROTEINS V. 37 388 1999 JRNL REFN ISSN 0887-3585 JRNL PMID 10591099 JRNL DOI 10.1002/(SICI)1097-0134(19991115)37:3<388::AID-PROT7>3.3.CO; JRNL DOI 2 2-6 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER REMARK 3 AUTHORS : BIOSYM REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: SIMULATED ANNEALING PROTOCOL ADOPTED REMARK 3 FROM NILGES ET AL. 1988, FEBS LETTERS, VOL. 239, PP129-136. REMARK 4 REMARK 4 1BK8 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000171852. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 292.5 REMARK 210 PH : 4.1 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY; TOCSY; DQFCOSY; E.COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : AM500 REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : DIANA/REDAC, DISCOVER REMARK 210 METHOD USED : DISTANCE GEOMETRY AND SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 500 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 25 REMARK 210 CONFORMERS, SELECTION CRITERIA : LEAST RESTRAINT VIOLATION AND REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: 2D HOMONUCLEAR 1H NMR WAS USED TO EXTRACT DISTANCE AND REMARK 210 TORSIONAL CONSTRAINTS. RMSD BACKBONE ATOMS 0.81 +/- 0.12. RMSD REMARK 210 ALL ATOMS 1.25 +/- 0.13. THE AMBER FORCEFIELD WAS USED FOR THE REMARK 210 SIMULATED ANNEALING. 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 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 LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 1 GLU A 4 CD GLU A 4 OE1 0.111 REMARK 500 1 GLU A 28 CD GLU A 28 OE2 0.110 REMARK 500 1 GLU A 39 CD GLU A 39 OE1 0.109 REMARK 500 2 GLU A 4 CD GLU A 4 OE1 0.107 REMARK 500 2 GLU A 28 CD GLU A 28 OE1 0.111 REMARK 500 2 GLU A 39 CD GLU A 39 OE1 0.107 REMARK 500 3 GLU A 4 CD GLU A 4 OE1 0.107 REMARK 500 3 GLU A 28 CD GLU A 28 OE2 0.111 REMARK 500 3 GLU A 39 CD GLU A 39 OE2 0.106 REMARK 500 4 GLU A 4 CD GLU A 4 OE1 0.108 REMARK 500 4 GLU A 28 CD GLU A 28 OE1 0.108 REMARK 500 4 GLU A 39 CD GLU A 39 OE1 0.107 REMARK 500 5 GLU A 4 CD GLU A 4 OE1 0.107 REMARK 500 5 GLU A 28 CD GLU A 28 OE1 0.108 REMARK 500 5 GLU A 39 CD GLU A 39 OE2 0.107 REMARK 500 6 GLU A 4 CD GLU A 4 OE1 0.109 REMARK 500 6 GLU A 28 CD GLU A 28 OE1 0.107 REMARK 500 6 GLU A 39 CD GLU A 39 OE2 0.107 REMARK 500 7 GLU A 4 CD GLU A 4 OE1 0.108 REMARK 500 7 GLU A 28 CD GLU A 28 OE2 0.107 REMARK 500 7 GLU A 39 CD GLU A 39 OE1 0.108 REMARK 500 8 GLU A 4 CD GLU A 4 OE1 0.112 REMARK 500 8 GLU A 28 CD GLU A 28 OE2 0.106 REMARK 500 8 GLU A 39 CD GLU A 39 OE2 0.106 REMARK 500 9 GLU A 4 CD GLU A 4 OE1 0.110 REMARK 500 9 GLU A 28 CD GLU A 28 OE2 0.110 REMARK 500 9 GLU A 39 CD GLU A 39 OE1 0.107 REMARK 500 10 GLU A 4 CD GLU A 4 OE1 0.107 REMARK 500 10 GLU A 28 CD GLU A 28 OE1 0.107 REMARK 500 10 GLU A 39 CD GLU A 39 OE1 0.107 REMARK 500 11 GLU A 4 CD GLU A 4 OE1 0.108 REMARK 500 11 GLU A 28 CD GLU A 28 OE2 0.106 REMARK 500 11 GLU A 39 CD GLU A 39 OE1 0.108 REMARK 500 12 GLU A 4 CD GLU A 4 OE1 0.111 REMARK 500 12 GLU A 28 CD GLU A 28 OE2 0.110 REMARK 500 12 GLU A 39 CD GLU A 39 OE1 0.107 REMARK 500 13 GLU A 4 CD GLU A 4 OE1 0.107 REMARK 500 13 GLU A 28 CD GLU A 28 OE2 0.107 REMARK 500 13 GLU A 39 CD GLU A 39 OE1 0.108 REMARK 500 14 GLU A 4 CD GLU A 4 OE1 0.106 REMARK 500 14 GLU A 28 CD GLU A 28 OE1 0.107 REMARK 500 14 GLU A 39 CD GLU A 39 OE1 0.107 REMARK 500 15 GLU A 4 CD GLU A 4 OE1 0.107 REMARK 500 15 GLU A 28 CD GLU A 28 OE2 0.108 REMARK 500 15 GLU A 39 CD GLU A 39 OE2 0.106 REMARK 500 16 GLU A 4 CD GLU A 4 OE1 0.108 REMARK 500 16 GLU A 28 CD GLU A 28 OE1 0.110 REMARK 500 16 GLU A 39 CD GLU A 39 OE1 0.108 REMARK 500 17 GLU A 4 CD GLU A 4 OE1 0.106 REMARK 500 17 GLU A 28 CD GLU A 28 OE2 0.107 REMARK 500 REMARK 500 THIS ENTRY HAS 75 BOND DEVIATIONS. 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 1 CYS A 35 CA - CB - SG ANGL. DEV. = 9.0 DEGREES REMARK 500 4 CYS A 35 CA - CB - SG ANGL. DEV. = 7.6 DEGREES REMARK 500 5 CYS A 2 CA - CB - SG ANGL. DEV. = 10.2 DEGREES REMARK 500 10 CYS A 35 CA - CB - SG ANGL. DEV. = 6.6 DEGREES REMARK 500 14 CYS A 35 CA - CB - SG ANGL. DEV. = 9.0 DEGREES REMARK 500 17 CYS A 2 CA - CB - SG ANGL. DEV. = 9.8 DEGREES REMARK 500 20 CYS A 35 CA - CB - SG ANGL. DEV. = 8.0 DEGREES REMARK 500 22 CYS A 35 CA - CB - SG ANGL. DEV. = 8.6 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 1 SER A 7 105.50 -54.99 REMARK 500 1 SER A 11 -131.96 -90.86 REMARK 500 1 GLN A 23 47.48 -79.02 REMARK 500 1 CYS A 24 -48.46 -166.26 REMARK 500 1 GLU A 28 -142.09 -73.88 REMARK 500 1 LYS A 29 51.68 -160.46 REMARK 500 1 HIS A 32 -164.26 -161.34 REMARK 500 1 ASN A 49 45.94 32.25 REMARK 500 2 CYS A 2 86.53 -61.86 REMARK 500 2 PRO A 6 174.87 -54.86 REMARK 500 2 GLN A 8 -64.18 -94.25 REMARK 500 2 GLN A 23 33.28 -78.50 REMARK 500 2 CYS A 24 -50.54 -132.59 REMARK 500 2 TRP A 27 -79.82 -75.17 REMARK 500 2 LYS A 29 57.81 131.71 REMARK 500 2 PHE A 48 -75.97 -84.62 REMARK 500 2 ASN A 49 33.93 -84.75 REMARK 500 3 CYS A 2 97.94 -49.74 REMARK 500 3 SER A 7 105.49 -54.48 REMARK 500 3 TRP A 10 76.56 -65.65 REMARK 500 3 GLU A 28 -148.51 -78.36 REMARK 500 3 LYS A 29 52.83 -161.50 REMARK 500 3 ASN A 40 -15.33 69.23 REMARK 500 3 ASN A 49 19.41 59.50 REMARK 500 4 GLN A 23 34.75 -75.31 REMARK 500 4 CYS A 24 -49.32 -144.42 REMARK 500 4 GLU A 28 -135.87 -81.13 REMARK 500 4 LYS A 29 59.56 -161.93 REMARK 500 4 ASN A 49 42.98 31.51 REMARK 500 5 SER A 7 111.29 -35.16 REMARK 500 5 GLN A 8 -93.89 -92.46 REMARK 500 5 GLU A 28 -155.66 -73.95 REMARK 500 5 LYS A 29 55.92 -161.28 REMARK 500 6 CYS A 2 81.32 -62.14 REMARK 500 6 GLU A 4 71.24 40.79 REMARK 500 6 SER A 7 108.37 -51.59 REMARK 500 6 GLN A 8 -61.83 -102.14 REMARK 500 6 GLU A 28 -148.97 -80.07 REMARK 500 6 LYS A 29 50.50 -161.55 REMARK 500 6 ALA A 34 136.62 -170.28 REMARK 500 6 ASN A 40 -13.59 69.90 REMARK 500 7 CYS A 2 95.95 -56.94 REMARK 500 7 SER A 7 104.27 -53.97 REMARK 500 7 SER A 11 55.85 38.96 REMARK 500 7 GLN A 23 34.26 -75.69 REMARK 500 7 CYS A 24 -48.89 -146.59 REMARK 500 7 GLU A 28 -143.38 -75.01 REMARK 500 7 LYS A 29 56.99 -161.85 REMARK 500 7 ASN A 49 19.63 53.78 REMARK 500 8 CYS A 2 81.13 -64.17 REMARK 500 REMARK 500 THIS ENTRY HAS 173 RAMACHANDRAN OUTLIERS. 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 TRP A 27 GLU A 28 2 -147.03 REMARK 500 CYS A 2 ASN A 3 6 -149.09 REMARK 500 TRP A 27 GLU A 28 12 -144.73 REMARK 500 ASN A 3 GLU A 4 15 124.91 REMARK 500 TRP A 27 GLU A 28 15 -148.48 REMARK 500 GLU A 28 LYS A 29 18 149.47 REMARK 500 ASN A 3 GLU A 4 21 140.38 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 4 TYR A 47 0.10 SIDE CHAIN REMARK 500 5 TYR A 47 0.08 SIDE CHAIN REMARK 500 7 TYR A 47 0.09 SIDE CHAIN REMARK 500 12 TYR A 47 0.12 SIDE CHAIN REMARK 500 15 TYR A 47 0.08 SIDE CHAIN REMARK 500 19 PHE A 48 0.09 SIDE CHAIN REMARK 500 20 TYR A 47 0.08 SIDE CHAIN REMARK 500 22 TYR A 47 0.10 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: 1 REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: SITE IMPORTANT FOR ANTIFUNGAL ACTIVITY. SEE REMARK 800 REMARK 6. DBREF 1BK8 A 1 50 UNP Q7M1F3 Q7M1F3_AESHI 1 50 SEQRES 1 A 50 LEU CYS ASN GLU ARG PRO SER GLN THR TRP SER GLY ASN SEQRES 2 A 50 CYS GLY ASN THR ALA HIS CYS ASP LYS GLN CYS GLN ASP SEQRES 3 A 50 TRP GLU LYS ALA SER HIS GLY ALA CYS HIS LYS ARG GLU SEQRES 4 A 50 ASN HIS TRP LYS CYS PHE CYS TYR PHE ASN CYS HELIX 1 H1 THR A 17 TRP A 27 1 11 SHEET 1 S1 3 CYS A 2 SER A 7 0 SHEET 2 S1 3 TRP A 42 PHE A 48 -1 O PHE A 48 N ASN A 3 SHEET 3 S1 3 HIS A 32 LYS A 37 -1 N HIS A 32 O TYR A 47 SSBOND 1 CYS A 2 CYS A 50 1555 1555 2.08 SSBOND 2 CYS A 14 CYS A 35 1555 1555 2.08 SSBOND 3 CYS A 20 CYS A 44 1555 1555 2.06 SSBOND 4 CYS A 24 CYS A 46 1555 1555 2.08 SITE 1 1 10 THR A 9 TRP A 27 LYS A 37 GLU A 39 SITE 2 1 10 LYS A 43 SER A 11 HIS A 41 PHE A 48 SITE 3 1 10 GLN A 8 ARG A 38 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