HEADER ANTIBIOTIC 09-JUN-05 1ZY6
TITLE MEMBRANE-BOUND DIMER STRUCTURE OF PROTEGRIN-1 (PG-1), A BETA-HAIRPIN
TITLE 2 ANTIMICROBIAL PEPTIDE IN LIPID BILAYERS FROM ROTATIONAL-ECHO DOUBLE-
TITLE 3 RESONANCE SOLID-STATE NMR
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: PROTEGRIN 1;
COMPND 3 CHAIN: A, B;
COMPND 4 SYNONYM: PG-1, NEUTROPHIL PEPTIDE 1;
COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 OTHER_DETAILS: BIOLOGICAL SEQUENCE WITH AMIDATED C-TERMINUS
KEYWDS BETA-HAIRPIN, SOLID STATE NMR, ANTIBIOTIC
EXPDTA SOLID-STATE NMR
AUTHOR X.WU,R.MANI,M.TANG,J.J.BUFFY,A.J.WARING,M.A.SHERMAN,M.HONG
REVDAT 5 13-NOV-24 1ZY6 1 REMARK
REVDAT 4 02-MAR-22 1ZY6 1 REMARK SEQADV LINK
REVDAT 3 24-FEB-09 1ZY6 1 VERSN
REVDAT 2 18-JUL-06 1ZY6 1 JRNL
REVDAT 1 13-JUN-06 1ZY6 0
JRNL AUTH R.MANI,M.TANG,X.WU,J.J.BUFFY,A.J.WARING,M.A.SHERMAN,M.HONG
JRNL TITL MEMBRANE-BOUND DIMER STRUCTURE OF A BETA-HAIRPIN
JRNL TITL 2 ANTIMICROBIAL PEPTIDE FROM ROTATIONAL-ECHO DOUBLE-RESONANCE
JRNL TITL 3 SOLID-STATE NMR.
JRNL REF BIOCHEMISTRY V. 45 8341 2006
JRNL REFN ISSN 0006-2960
JRNL PMID 16819833
JRNL DOI 10.1021/BI060305B
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : SIMPSON, MODELLER 6.1
REMARK 3 AUTHORS : BAK, RASMUSSEN, NIELSEN (SIMPSON), SALI, BLUNDELL
REMARK 3 (MODELLER)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: TWO-SPIN REDOR CURVES WERE SIMULATED
REMARK 3 USING A FORTRAN PROGRAM. THREE-SPIN REDOR CURVES FOR THE C -F
REMARK 3 EXPERIMENT WERE SIMULATED USING THE SIMPSON PROGRAM. THE INPUT
REMARK 3 DISTANCES AND ANGLES IN THE THREE-SPIN SIMULATION WERE OBTAINED
REMARK 3 FROM MODEL BUILDING. THE SIMULATIONS ASSUMED DELTA-FUNCTION
REMARK 3 PULSES FOR ALL PI PULSES. MODELS THAT WERE POTENTIALLY
REMARK 3 CONSISTENT WITH ALL THE EXPERIMENTALLY MEASURED DISTANCES WERE
REMARK 3 CREATED USING MODELLER. IN ADDITION TO THE REDOR-BASED
REMARK 3 RESTRAINTS, THE INPUT FILE INCLUDED A RESTRAINT TO PRESERVE THE
REMARK 3 INTRAMOLECULAR HYDROGEN BOND LADDER OF EACH MONOMER, AND A
REMARK 3 RESTRAINT TO MAINTAIN MONOMER SYMMETRY.
REMARK 4
REMARK 4 1ZY6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-JUN-05.
REMARK 100 THE DEPOSITION ID IS D_1000033257.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 233
REMARK 210 PH : NULL
REMARK 210 IONIC STRENGTH : NULL
REMARK 210 PRESSURE : AMBIENT
REMARK 210 SAMPLE CONTENTS : 1:1 MOLAR MIXTURE OF [13C-CYS15]
REMARK 210 PG-1 AND [15N-CYS15] PG-1; [4-
REMARK 210 19F-PHE12, 13C-VAL16] PG-1
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : ROTATIONAL-ECHO DOUBLE RESONANCE
REMARK 210 (REDOR) NMR TECHNIQUE, WHICH
REMARK 210 MEASURES DISTANCES BETWEEN
REMARK 210 HETERONUCLEAR SPINS
REMARK 210 SPECTROMETER FIELD STRENGTH : 400 MHZ
REMARK 210 SPECTROMETER MODEL : DSX 400
REMARK 210 SPECTROMETER MANUFACTURER : BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : NULL
REMARK 210 METHOD USED : DISTANCE GEOMETRY; SIMULATED
REMARK 210 ANNEALING
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 100
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1
REMARK 210 CONFORMERS, SELECTION CRITERIA : LEAST VIOLATIONS
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL
REMARK 210
REMARK 210 REMARK: SOLID STATE NMR WAS PERFORMED AT 400.49 MHZ FOR 1H, 376.8
REMARK 210 MHZ FOR 19F, 100.72 MHZ FOR 13C, AND 40.58 MHZ FOR 15N. THE 15N{
REMARK 210 13C} AND 13C{1H} REDOR EXPERIMENTS WERE CARRIED OUT ON A 1H/13C/
REMARK 210 15N TRIPLE RESONANCE MAS PROBE. SPINNING SPEEDS WERE REGULATED
REMARK 210 TO 3 HZ USING A PNEUMATIC CONTROL UNIT. 13C AND 15N CHEMICAL
REMARK 210 SHIFTS WERE REFERENCED EXTERNALLY TO THE 13C SIGNAL OF ALPHA-GLY
REMARK 210 AT 176.4 PPM ON THE TMS SCALE AND THE 15N SIGNAL OF N-ACETYL-
REMARK 210 VALINE AT 122 PPM, RESPECTIVELY. THE 13C{19F} REDOR EXPERIMENTS,
REMARK 210 WHERE THE NUCLEUS IN THE BRACKET IS THE UNOBSERVED DEPHASING
REMARK 210 SPIN, WAS CONDUCTED ON A 4-MM MAGIC-ANGLE SPINNING (MAS) PROBE
REMARK 210 EQUIPPED WITH A BRUKER HFX UNIT, WHICH ALLOWS SIMULTANEOUS
REMARK 210 TUNING OF 1H AND 19F ON THE 1H CHANNEL.
REMARK 217
REMARK 217 SOLID STATE NMR STUDY
REMARK 217 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLID
REMARK 217 STATE NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT
REMARK 217 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON
REMARK 217 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: DIMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B
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: 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 ARG A 10 -111.64 64.69
REMARK 500 ARG B 10 -133.73 61.62
REMARK 500 PHE B 12 110.63 -160.59
REMARK 500
REMARK 500 REMARK: NULL
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NH2 A 19
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NH2 B 19
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1PG1 RELATED DB: PDB
REMARK 900 SOLUTION STRUCTURE OF PROTEGRIN-1, A BROAD-SPECTRUM ANTIMICROBIAL
REMARK 900 PEPTIDE FROM PORCINE LEUKOCYTES.
DBREF 1ZY6 A 1 18 UNP P32194 PG1_PIG 131 148
DBREF 1ZY6 B 1 18 UNP P32194 PG1_PIG 131 148
SEQADV 1ZY6 NH2 A 19 UNP P32194 AMIDATION
SEQADV 1ZY6 NH2 B 19 UNP P32194 AMIDATION
SEQRES 1 A 19 ARG GLY GLY ARG LEU CYS TYR CYS ARG ARG ARG PHE CYS
SEQRES 2 A 19 VAL CYS VAL GLY ARG NH2
SEQRES 1 B 19 ARG GLY GLY ARG LEU CYS TYR CYS ARG ARG ARG PHE CYS
SEQRES 2 B 19 VAL CYS VAL GLY ARG NH2
HET NH2 A 19 3
HET NH2 B 19 3
HETNAM NH2 AMINO GROUP
FORMUL 1 NH2 2(H2 N)
SHEET 1 A 4 LEU A 5 ARG A 9 0
SHEET 2 A 4 PHE A 12 VAL A 16 -1 O PHE A 12 N ARG A 9
SHEET 3 A 4 PHE B 12 VAL B 16 1 O CYS B 15 N CYS A 15
SHEET 4 A 4 LEU B 5 CYS B 8 -1 N TYR B 7 O VAL B 14
SSBOND 1 CYS A 6 CYS A 15 1555 1555 2.05
SSBOND 2 CYS A 8 CYS A 13 1555 1555 2.04
SSBOND 3 CYS B 6 CYS B 15 1555 1555 2.04
SSBOND 4 CYS B 8 CYS B 13 1555 1555 2.04
LINK C ARG A 18 N NH2 A 19 1555 1555 1.32
LINK C ARG B 18 N NH2 B 19 1555 1555 1.32
SITE 1 AC1 2 GLY A 2 ARG A 18
SITE 1 AC2 2 GLY B 2 ARG B 18
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