HEADER MEMBRANE PROTEIN 09-DEC-98 1M23 TITLE STRUCTURE OF THE DIMERIZED CYTOPLASMIC DOMAIN OF P23 IN SOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (P23); COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CYTOPLASMIC DOMAIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THE PROTEIN WAS CHEMICALLY SYNTHESIZED FROM THE GOLGI SOURCE 4 STACK OF THE ER (ENDOPLASMIC RETICULUM) OF NEW ZEALAND WHITE RABBIT SOURCE 5 (ORYCTOLAGUS CUNICULUS) LIVER CELLS. KEYWDS TRANSPORT, PROTEIN TRANSPORT, TRANSMEMBRANE, GLYCOPROTEIN, VESICULAR KEYWDS 2 TRANSPORT, COP, COATOMER, GOLGI STACK, SOLUTION STRUCTURE, P23 KEYWDS 3 FAMILY, MEMBRANE PROTEIN EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR M.WEIDLER,C.REINHARD,F.WIELAND,P.ROESCH REVDAT 5 27-DEC-23 1M23 1 REMARK REVDAT 4 23-FEB-22 1M23 1 REMARK REVDAT 3 24-FEB-09 1M23 1 VERSN REVDAT 2 01-APR-03 1M23 1 JRNL REVDAT 1 29-SEP-99 1M23 0 JRNL AUTH C.REINHARD,C.HARTER,M.BREMSER,B.BRUGGER,K.SOHN,J.B.HELMS, JRNL AUTH 2 F.WIELAND JRNL TITL RECEPTOR-INDUCED POLYMERIZATION OF COATOMER. JRNL REF PROC.NATL.ACAD.SCI.USA V. 96 1224 1999 JRNL REFN ISSN 0027-8424 JRNL PMID 9990005 JRNL DOI 10.1073/PNAS.96.4.1224 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.840 REMARK 3 AUTHORS : BRUNGER, NILGES REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: STRATEGY USED FOR NMR STRUCTURE REMARK 3 CALCULATION: EXPERIMENTAL RESTRAINTS FOR THE STRUCTURE REMARK 3 CALCULATIONS INITIALLY, FREQUENCY DEGENERATED NOESY CROSS-PEAKS REMARK 3 WERE INCORPORATED INTO THE STRUCTURE CALCULATION AS 'AMBIGUOUS'. REMARK 3 SUBSEQUENTLY, THE PROTON-PROTON DISTANCES IN THE CALCULATED REMARK 3 STRUCTURES WERE DETERMINED USING THE PROGRAM 'BACKCALC_DB 2.0' REMARK 3 (SOFTWARE SYMBIOSE, INC., BAYREUTH, GERMANY) AND COMPARED WITH REMARK 3 THE COMBINATIONS OF DISTANCES POSSIBLE FOR EACH FREQUENCY REMARK 3 DEGENERATED NOESY CROSS-PEAK. IF ONLY ONE OF THE POSSIBLE REMARK 3 DISTANCE COMBINATIONS WAS FULFILLED IN MORE THAN 50% OF THE REMARK 3 CALCULATED STRUCTURES, THE DISTANCE INFORMATION WAS USED IN REMARK 3 FURTHER STRUCTURE CALCULATIONS. THIS PROCEDURE WAS REPEATED REMARK 3 SEVERAL TIMES, LEADING TO A TOTAL OF 223 INTRARESIDUAL AND 249 REMARK 3 INTERRESIDUAL NOE CONNECTIVITIES. STRUCTURE CALCULATIONS REMARK 3 STRUCTURES CALCULATIONS WERE PERFORMED USING A MODIFIED AB REMARK 3 INITIO SIMULATED ANNEALING PROTOCOL (NILGES, UNPUBLISHED) WITH X- REMARK 3 PLOR V3.840. THE CALCULATION STRATEGY INCLUDES FLOATING REMARK 3 ASSIGNMENT OF PROCHIRAL GROUPS AND A REDUCED PRESENTATION FOR REMARK 3 NON-BONDED INTERACTIONS FOR PART OF THE CALCULATION TO INCREASE REMARK 3 EFFICIENCY. A MORE DETAILED DESCRIPTION OF THE PROTOCOL IS GIVEN REMARK 3 IN KHARRAT ET AL. (EMBO J. 14 (1995) 3572-84). STRUCTURE REMARK 3 PARAMETERS WERE EXTRACTED FROM THE STANDARD FILES PARALLHDG.PRO REMARK 3 AND TOPALLHDG.PRO OF X-PLOR V3.840. IN EACH ROUND OF THE REMARK 3 STRUCTURE CALCULATION 100 STRUCTURES WERE CALCULATED. OF THE 100 REMARK 3 STRUCTURES RESULTING FROM THE FINAL ROUND OF STRUCTURE REMARK 3 CALCULATION, THOSE 30 STRUCTURES THAT SHOWED THE LOWEST TOTAL REMARK 3 ENERGY VALUES WERE SELECTED FOR FURTHER CHARACTERIZATION. REMARK 4 REMARK 4 1M23 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-JUL-99. REMARK 100 THE DEPOSITION ID IS D_1000007011. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 280 REMARK 210 PH : 3.6 REMARK 210 IONIC STRENGTH : 650 MM REMARK 210 PRESSURE : 10E+5 PA ATM REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY; COSY; CLEAN-TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : DRX 600 REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NDEE 2.0, X-PLOR 3.840 REMARK 210 METHOD USED : SIMULATED ANNEALING, RESTRAINED REMARK 210 MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 30 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : ENERGY, AGREEMENT WITH REMARK 210 EXPERIMENTAL DATA 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 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: 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 LEU A 2 -14.40 -44.91 REMARK 500 1 PHE A 6 -64.92 -93.42 REMARK 500 1 ALA A 8 -93.59 -62.37 REMARK 500 2 ALA A 8 -91.94 -80.45 REMARK 500 3 PHE A 6 -60.02 -91.84 REMARK 500 3 ALA A 8 -94.60 -80.04 REMARK 500 4 PHE A 6 -60.91 -91.21 REMARK 500 4 ALA A 8 -94.03 -68.64 REMARK 500 5 PHE A 6 -64.27 -91.85 REMARK 500 5 ALA A 8 -95.01 -80.83 REMARK 500 6 ALA A 8 -91.59 -71.20 REMARK 500 7 ALA A 8 -92.04 -74.04 REMARK 500 8 PHE A 6 -62.93 -93.50 REMARK 500 8 ALA A 8 -90.11 -79.81 REMARK 500 9 ALA A 8 -94.02 -69.84 REMARK 500 10 PHE A 6 -62.95 -93.26 REMARK 500 10 ALA A 8 -89.42 -77.24 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 1 ARG A 3 0.28 SIDE CHAIN REMARK 500 1 ARG A 4 0.32 SIDE CHAIN REMARK 500 2 ARG A 3 0.27 SIDE CHAIN REMARK 500 2 ARG A 4 0.27 SIDE CHAIN REMARK 500 3 ARG A 3 0.23 SIDE CHAIN REMARK 500 3 ARG A 4 0.24 SIDE CHAIN REMARK 500 4 ARG A 3 0.32 SIDE CHAIN REMARK 500 4 ARG A 4 0.26 SIDE CHAIN REMARK 500 5 ARG A 3 0.21 SIDE CHAIN REMARK 500 5 ARG A 4 0.13 SIDE CHAIN REMARK 500 6 ARG A 3 0.28 SIDE CHAIN REMARK 500 6 ARG A 4 0.13 SIDE CHAIN REMARK 500 7 ARG A 3 0.31 SIDE CHAIN REMARK 500 7 ARG A 4 0.16 SIDE CHAIN REMARK 500 8 ARG A 3 0.30 SIDE CHAIN REMARK 500 9 ARG A 3 0.32 SIDE CHAIN REMARK 500 9 ARG A 4 0.32 SIDE CHAIN REMARK 500 10 ARG A 3 0.30 SIDE CHAIN REMARK 500 10 ARG A 4 0.20 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 1M23 A 2 13 UNP Q28735 TMP21_RABIT 207 218 SEQRES 1 A 13 TYR LEU ARG ARG PHE PHE LYS ALA LYS LYS LEU ILE GLU HELIX 1 1 LEU A 2 LEU A 11 1 10 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