PDB Short entry for 1C01 HEADER ANTIMICROBIAL PROTEIN 13-JUL-99 1C01 TITLE SOLUTION STRUCTURE OF MIAMP1, A PLANT ANTIMICROBIAL PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: ANTIMICROBIAL PEPTIDE 1; COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MACADAMIA INTEGRIFOLIA; SOURCE 3 ORGANISM_TAXID: 60698; SOURCE 4 ORGAN: NUT KERNEL KEYWDS GREEK KEY, BETA-BARREL, ANTIMICROBIAL PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR A.M.MCMANUS,K.J.NIELSEN,J.P.MARCUS,S.J.HARRISON,J.L.GREEN, AUTHOR 2 J.M.MANNERS,D.J.CRAIK REVDAT 3 16-FEB-22 1C01 1 REMARK REVDAT 2 24-FEB-09 1C01 1 VERSN REVDAT 1 19-JUL-00 1C01 0 JRNL AUTH A.M.MCMANUS,K.J.NIELSEN,J.P.MARCUS,S.J.HARRISON,J.L.GREEN, JRNL AUTH 2 J.M.MANNERS,D.J.CRAIK JRNL TITL MIAMP1, A NOVEL PROTEIN FROM MACADAMIA INTEGRIFOLIA ADOPTS A JRNL TITL 2 GREEK KEY BETA-BARREL FOLD UNIQUE AMONGST PLANT JRNL TITL 3 ANTIMICROBIAL PROTEINS. JRNL REF J.MOL.BIOL. V. 293 629 1999 JRNL REFN ISSN 0022-2836 JRNL PMID 10543955 JRNL DOI 10.1006/JMBI.1999.3163 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 2.1, X-PLOR 3.1 REMARK 3 AUTHORS : BRUKER (XWINNMR), BRUNGER (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 THE STRUCTURES WERE CALCULATED FROM 1571 DISTANCE RESTRAINTS, 31 REMARK 3 HYDROGEN BOND REMARK 3 RESTRAINTS AND 43 DIHEDRAL ANGLE RESTRAINTS REMARK 4 REMARK 4 1C01 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-JUL-99. REMARK 100 THE DEPOSITION ID IS D_1000009337. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 308; 283 REMARK 210 PH : 5.0; 5.0 REMARK 210 IONIC STRENGTH : 1.5 MM; 1.5 MM REMARK 210 PRESSURE : 11 ATM; 11 ATM REMARK 210 SAMPLE CONTENTS : 1.5 MM ANTIMICROBIAL PROTEIN; REMARK 210 90% H2O, 10% D2O; 1.5 MM REMARK 210 ANTIMICROBIAL PROTEIN U-15N; 90% REMARK 210 H2O, 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; DQF-COSY; 1H-15N HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 750 MHZ REMARK 210 SPECTROMETER MODEL : DMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-EASY 1.3.7, X-PLOR 3.1 REMARK 210 METHOD USED : HIGH TEMPERATURE MOLECULAR REMARK 210 DYNAMICS/SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 8 REMARK 210 REMARK 210 REMARK: REMARK 210 THIS STRUCTURE WAS DETERMINED USING STANDARD 2D HOMONUCLEAR AND REMARK 210 HETERONUCLEAR REMARK 210 TECHNIQUES 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 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 TRP A 6 CD1 - NE1 - CE2 ANGL. DEV. = 7.1 DEGREES REMARK 500 1 TRP A 69 CD1 - NE1 - CE2 ANGL. DEV. = 7.3 DEGREES REMARK 500 1 TRP A 69 NE1 - CE2 - CZ2 ANGL. DEV. = 7.2 DEGREES REMARK 500 2 TRP A 6 CD1 - NE1 - CE2 ANGL. DEV. = 7.1 DEGREES REMARK 500 2 TRP A 69 CG - CD1 - NE1 ANGL. DEV. = -6.0 DEGREES REMARK 500 2 TRP A 69 CD1 - NE1 - CE2 ANGL. DEV. = 7.3 DEGREES REMARK 500 2 TRP A 69 NE1 - CE2 - CZ2 ANGL. DEV. = 7.3 DEGREES REMARK 500 3 TRP A 6 CD1 - NE1 - CE2 ANGL. DEV. = 7.2 DEGREES REMARK 500 3 TRP A 6 NE1 - CE2 - CZ2 ANGL. DEV. = 7.4 DEGREES REMARK 500 3 TRP A 69 CD1 - NE1 - CE2 ANGL. DEV. = 7.3 DEGREES REMARK 500 3 TRP A 69 NE1 - CE2 - CZ2 ANGL. DEV. = 7.1 DEGREES REMARK 500 4 TRP A 6 CD1 - NE1 - CE2 ANGL. DEV. = 7.0 DEGREES REMARK 500 4 TRP A 69 CD1 - NE1 - CE2 ANGL. DEV. = 7.5 DEGREES REMARK 500 5 TRP A 6 CD1 - NE1 - CE2 ANGL. DEV. = 7.0 DEGREES REMARK 500 5 TRP A 6 NE1 - CE2 - CZ2 ANGL. DEV. = 6.8 DEGREES REMARK 500 5 TRP A 69 CD1 - NE1 - CE2 ANGL. DEV. = 7.2 DEGREES REMARK 500 6 TRP A 6 CD1 - NE1 - CE2 ANGL. DEV. = 7.0 DEGREES REMARK 500 6 TRP A 69 CD1 - NE1 - CE2 ANGL. DEV. = 7.5 DEGREES REMARK 500 6 TRP A 69 NE1 - CE2 - CZ2 ANGL. DEV. = 6.6 DEGREES REMARK 500 7 TRP A 6 CD1 - NE1 - CE2 ANGL. DEV. = 7.1 DEGREES REMARK 500 7 TRP A 69 CD1 - NE1 - CE2 ANGL. DEV. = 7.5 DEGREES REMARK 500 8 TRP A 6 CD1 - NE1 - CE2 ANGL. DEV. = 7.3 DEGREES REMARK 500 8 TRP A 6 NE1 - CE2 - CZ2 ANGL. DEV. = 7.2 DEGREES REMARK 500 8 CYS A 49 CA - CB - SG ANGL. DEV. = 7.0 DEGREES REMARK 500 8 TRP A 69 CD1 - NE1 - CE2 ANGL. DEV. = 7.3 DEGREES REMARK 500 9 TRP A 6 CD1 - NE1 - CE2 ANGL. DEV. = 7.1 DEGREES REMARK 500 9 TRP A 69 CG - CD1 - NE1 ANGL. DEV. = -6.0 DEGREES REMARK 500 9 TRP A 69 CD1 - NE1 - CE2 ANGL. DEV. = 7.4 DEGREES REMARK 500 9 TRP A 69 NE1 - CE2 - CZ2 ANGL. DEV. = 6.9 DEGREES REMARK 500 10 TRP A 6 CD1 - NE1 - CE2 ANGL. DEV. = 7.3 DEGREES REMARK 500 10 TRP A 6 NE1 - CE2 - CZ2 ANGL. DEV. = 6.7 DEGREES REMARK 500 10 CYS A 11 CA - CB - SG ANGL. DEV. = 8.8 DEGREES REMARK 500 10 TRP A 69 CD1 - NE1 - CE2 ANGL. DEV. = 7.3 DEGREES REMARK 500 10 TRP A 69 NE1 - CE2 - CZ2 ANGL. DEV. = 6.7 DEGREES REMARK 500 11 TRP A 6 CD1 - NE1 - CE2 ANGL. DEV. = 7.2 DEGREES REMARK 500 11 TRP A 69 CD1 - NE1 - CE2 ANGL. DEV. = 7.1 DEGREES REMARK 500 12 TRP A 6 CD1 - NE1 - CE2 ANGL. DEV. = 7.2 DEGREES REMARK 500 12 CYS A 11 CA - CB - SG ANGL. DEV. = 7.0 DEGREES REMARK 500 12 TRP A 69 CD1 - NE1 - CE2 ANGL. DEV. = 7.3 DEGREES REMARK 500 12 TRP A 69 NE1 - CE2 - CZ2 ANGL. DEV. = 6.9 DEGREES REMARK 500 13 TRP A 6 CD1 - NE1 - CE2 ANGL. DEV. = 7.1 DEGREES REMARK 500 13 TRP A 6 NE1 - CE2 - CZ2 ANGL. DEV. = 6.8 DEGREES REMARK 500 13 TRP A 69 CD1 - NE1 - CE2 ANGL. DEV. = 7.4 DEGREES REMARK 500 13 TRP A 69 NE1 - CE2 - CZ2 ANGL. DEV. = 7.0 DEGREES REMARK 500 14 TRP A 6 CD1 - NE1 - CE2 ANGL. DEV. = 7.2 DEGREES REMARK 500 14 TRP A 6 NE1 - CE2 - CZ2 ANGL. DEV. = 6.8 DEGREES REMARK 500 14 TRP A 69 CD1 - NE1 - CE2 ANGL. DEV. = 7.4 DEGREES REMARK 500 15 TRP A 6 CD1 - NE1 - CE2 ANGL. DEV. = 7.1 DEGREES REMARK 500 15 TRP A 69 CG - CD1 - NE1 ANGL. DEV. = -6.0 DEGREES REMARK 500 15 TRP A 69 CD1 - NE1 - CE2 ANGL. DEV. = 7.3 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 67 ANGLE DEVIATIONS. 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 CYS A 11 57.53 -96.87 REMARK 500 1 ASN A 13 -122.64 -173.53 REMARK 500 1 THR A 37 73.39 -174.82 REMARK 500 1 ALA A 47 150.58 -43.94 REMARK 500 1 CYS A 49 44.66 39.03 REMARK 500 1 SER A 50 37.70 -86.07 REMARK 500 1 HIS A 54 -59.00 -142.83 REMARK 500 2 CYS A 11 41.97 -93.07 REMARK 500 2 ASN A 12 -128.32 -124.41 REMARK 500 2 ASN A 13 -142.05 38.30 REMARK 500 2 GLN A 28 99.68 -51.43 REMARK 500 2 THR A 37 -35.26 -140.08 REMARK 500 2 CYS A 49 22.29 44.31 REMARK 500 2 SER A 50 45.51 -90.55 REMARK 500 2 PHE A 67 -146.17 -111.04 REMARK 500 2 GLN A 75 80.34 -61.61 REMARK 500 3 CYS A 11 48.23 -89.65 REMARK 500 3 ASN A 13 -146.47 171.71 REMARK 500 3 TYR A 18 78.70 -110.15 REMARK 500 3 LYS A 29 40.00 -80.56 REMARK 500 3 THR A 37 52.49 -167.42 REMARK 500 3 SER A 50 40.79 -83.93 REMARK 500 3 HIS A 54 -48.85 -146.59 REMARK 500 3 PHE A 67 -135.63 -123.49 REMARK 500 4 CYS A 11 44.83 -94.31 REMARK 500 4 ASN A 12 -129.30 -123.21 REMARK 500 4 ASN A 13 -144.31 38.20 REMARK 500 4 GLU A 16 118.51 -161.64 REMARK 500 4 THR A 37 -20.05 -168.48 REMARK 500 4 HIS A 54 -69.55 -139.30 REMARK 500 4 SER A 60 112.33 -38.05 REMARK 500 5 CYS A 11 53.40 -111.99 REMARK 500 5 ASN A 13 -144.72 178.31 REMARK 500 5 HIS A 27 14.87 -142.39 REMARK 500 5 LYS A 29 59.03 -90.10 REMARK 500 5 THR A 37 -39.67 -146.28 REMARK 500 5 SER A 50 34.73 -81.59 REMARK 500 5 ALA A 53 -169.08 -72.21 REMARK 500 5 HIS A 54 -59.41 -153.93 REMARK 500 5 SER A 60 117.08 -37.72 REMARK 500 5 PHE A 67 -169.87 -161.36 REMARK 500 6 CYS A 11 50.42 -93.30 REMARK 500 6 ASN A 12 -126.97 -134.64 REMARK 500 6 ASN A 13 -141.88 37.76 REMARK 500 6 THR A 37 66.68 -152.35 REMARK 500 6 CYS A 64 10.06 -147.39 REMARK 500 7 CYS A 11 54.98 -96.06 REMARK 500 7 ASN A 13 -150.29 -178.46 REMARK 500 7 SER A 59 127.25 -175.51 REMARK 500 7 SER A 60 111.19 -30.64 REMARK 500 REMARK 500 THIS ENTRY HAS 182 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 ASN A 65 PRO A 66 11 144.69 REMARK 500 REMARK 500 REMARK: NULL DBREF 1C01 A 1 76 UNP P80915 AMP1_MACIN 27 102 SEQRES 1 A 76 SER ALA PHE THR VAL TRP SER GLY PRO GLY CYS ASN ASN SEQRES 2 A 76 ARG ALA GLU ARG TYR SER LYS CYS GLY CYS SER ALA ILE SEQRES 3 A 76 HIS GLN LYS GLY GLY TYR ASP PHE SER TYR THR GLY GLN SEQRES 4 A 76 THR ALA ALA LEU TYR ASN GLN ALA GLY CYS SER GLY VAL SEQRES 5 A 76 ALA HIS THR ARG PHE GLY SER SER ALA ARG ALA CYS ASN SEQRES 6 A 76 PRO PHE GLY TRP LYS SER ILE PHE ILE GLN CYS HELIX 1 1 GLN A 46 SER A 50 5 5 SHEET 1 A 3 GLU A 16 TYR A 18 0 SHEET 2 A 3 ALA A 2 VAL A 5 -1 O PHE A 3 N TYR A 18 SHEET 3 A 3 TYR A 32 SER A 35 -1 N ASP A 33 O THR A 4 SHEET 1 B 4 GLY A 22 ALA A 25 0 SHEET 2 B 4 SER A 71 ILE A 74 -1 N ILE A 72 O SER A 24 SHEET 3 B 4 ALA A 41 TYR A 44 -1 O ALA A 42 N PHE A 73 SHEET 4 B 4 ALA A 53 PHE A 57 -1 N HIS A 54 O LEU A 43 SSBOND 1 CYS A 11 CYS A 64 1555 1555 2.02 SSBOND 2 CYS A 21 CYS A 76 1555 1555 2.02 SSBOND 3 CYS A 23 CYS A 49 1555 1555 2.02 CISPEP 1 GLY A 8 PRO A 9 1 8.00 CISPEP 2 GLY A 8 PRO A 9 2 17.92 CISPEP 3 GLY A 8 PRO A 9 3 9.98 CISPEP 4 GLY A 8 PRO A 9 4 17.61 CISPEP 5 GLY A 8 PRO A 9 5 8.71 CISPEP 6 GLY A 8 PRO A 9 6 13.03 CISPEP 7 GLY A 8 PRO A 9 7 7.68 CISPEP 8 GLY A 8 PRO A 9 8 19.97 CISPEP 9 GLY A 8 PRO A 9 9 19.35 CISPEP 10 GLY A 8 PRO A 9 10 13.95 CISPEP 11 GLY A 8 PRO A 9 11 12.43 CISPEP 12 GLY A 8 PRO A 9 12 16.91 CISPEP 13 GLY A 8 PRO A 9 13 18.09 CISPEP 14 GLY A 8 PRO A 9 14 25.62 CISPEP 15 GLY A 8 PRO A 9 15 18.29 CISPEP 16 GLY A 8 PRO A 9 16 20.71 CISPEP 17 GLY A 8 PRO A 9 17 12.37 CISPEP 18 GLY A 8 PRO A 9 18 14.77 CISPEP 19 GLY A 8 PRO A 9 19 17.00 CISPEP 20 GLY A 8 PRO A 9 20 11.15 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