HEADER STRUCTURAL PROTEIN/RNA 08-FEB-05 1YSH TITLE LOCALIZATION AND DYNAMIC BEHAVIOR OF RIBOSOMAL PROTEIN L30E COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (28-MER); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: RNA (34-MER); COMPND 7 CHAIN: F; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: RNA (101-MER); COMPND 11 CHAIN: B; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 4; COMPND 14 MOLECULE: RIBOSOMAL PROTEIN L30; COMPND 15 CHAIN: C; COMPND 16 MOL_ID: 5; COMPND 17 MOLECULE: RIBOSOMAL PROTEIN L37A; COMPND 18 CHAIN: D; COMPND 19 MOL_ID: 6; COMPND 20 MOLECULE: 40S RIBOSOMAL PROTEIN S13; COMPND 21 CHAIN: E SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 8 ORGANISM_TAXID: 32630; SOURCE 9 MOL_ID: 3; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 12 ORGANISM_TAXID: 32630; SOURCE 13 MOL_ID: 4; SOURCE 14 ORGANISM_SCIENTIFIC: TRITICUM AESTIVUM; SOURCE 15 ORGANISM_COMMON: BREAD WHEAT; SOURCE 16 ORGANISM_TAXID: 4565; SOURCE 17 MOL_ID: 5; SOURCE 18 ORGANISM_SCIENTIFIC: ORYZA SATIVA; SOURCE 19 ORGANISM_COMMON: RICE; SOURCE 20 ORGANISM_TAXID: 4530; SOURCE 21 MOL_ID: 6; SOURCE 22 ORGANISM_SCIENTIFIC: ORYZA SATIVA; SOURCE 23 ORGANISM_COMMON: RICE; SOURCE 24 ORGANISM_TAXID: 4530 KEYWDS STRUCTURAL PROTEIN, RNA, STRUCTURAL PROTEIN-RNA COMPLEX EXPDTA ELECTRON MICROSCOPY AUTHOR M.HALIC,T.BECKER,J.FRANK,C.M.SPAHN,R.BECKMANN REVDAT 4 09-OCT-24 1YSH 1 REMARK REVDAT 3 18-DEC-19 1YSH 1 SOURCE REMARK REVDAT 2 24-FEB-09 1YSH 1 VERSN REVDAT 1 05-JUL-05 1YSH 0 JRNL AUTH M.HALIC,T.BECKER,J.FRANK,C.M.SPAHN,R.BECKMANN JRNL TITL LOCALIZATION AND DYNAMIC BEHAVIOR OF RIBOSOMAL PROTEIN L30E JRNL REF NAT.STRUCT.MOL.BIOL. V. 12 467 2005 JRNL REFN ISSN 1545-9993 JRNL PMID 15864315 JRNL DOI 10.1038/NSMB933 REMARK 2 REMARK 2 RESOLUTION. 9.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : SPIDER REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : NULL REMARK 3 REFINEMENT PROTOCOL : NULL REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : NULL REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : 2.040 REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 9.500 REMARK 3 NUMBER OF PARTICLES : 21000 REMARK 3 CTF CORRECTION METHOD : NULL REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 1YSH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ. REMARK 100 THE DEPOSITION ID IS D_1000031879. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : SINGLE PARTICLE REMARK 245 SPECIMEN TYPE : VITREOUS ICE (CRYO EM) REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : PARTICLE REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : 80S WHEAT GERM RIBOSOME REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : HOLEY CARBON REMARK 245 SAMPLE VITRIFICATION DETAILS : PLUNGED INTO ETHANE REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.40 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : 01-JAN-00 REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : 95.00 REMARK 245 MICROSCOPE MODEL : FEI TECNAI F30 REMARK 245 DETECTOR TYPE : KODAK SO-163 FILM REMARK 245 MINIMUM DEFOCUS (NM) : 7000.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 45000.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : 0.00 REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : 0.00 REMARK 245 NOMINAL CS : 2.00 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 1000.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 38250 REMARK 245 CALIBRATED MAGNIFICATION : 38300 REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 300 REMARK 245 IMAGING DETAILS : SAMPLES WERE MAINTAINED AT REMARK 245 LIQUID NITROGEN TEMPERATURES IN THE ELECTRON MICROSCOPE REMARK 247 REMARK 247 ELECTRON MICROSCOPY REMARK 247 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM ELECTRON REMARK 247 MICROSCOPY DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE REMARK 247 THAT CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES REMARK 247 ON THESE RECORDS ARE MEANINGLESS EXCEPT FOR THE CALCULATION REMARK 247 OF THE STRUCTURE FACTORS. 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: HEXAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, F, B, C, D, E 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 C F1579 O5' C5' C4' O4' C3' O3' C2' REMARK 470 C F1579 O2' C1' N1 C2 O2 N3 C4 REMARK 470 C F1579 N4 C5 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O4' A A 806 CE1 HIS E 123 0.30 REMARK 500 ND2 ASN C 73 CB TYR C 83 0.60 REMARK 500 O3' G B 668 CE LYS E 107 0.64 REMARK 500 O ALA E 126 NZ LYS E 140 0.70 REMARK 500 O6 G F 1604 CG PRO C 48 0.72 REMARK 500 CG2 THR C 78 C LYS C 82 0.78 REMARK 500 CG HIS C 67 OG1 THR C 104 0.80 REMARK 500 C ALA E 126 CE LYS E 140 0.84 REMARK 500 CD2 HIS C 67 OG1 THR C 104 0.86 REMARK 500 N7 G F 1604 NH1 ARG C 51 1.01 REMARK 500 O ALA E 126 CE LYS E 140 1.04 REMARK 500 C6 G F 1604 CG PRO C 48 1.04 REMARK 500 C LYS C 21 CB ASP C 93 1.06 REMARK 500 CG2 THR C 78 N TYR C 83 1.09 REMARK 500 C3' G B 668 CE LYS E 107 1.10 REMARK 500 O PRO E 85 N GLU E 86 1.13 REMARK 500 N LYS C 1 N ALA C 2 1.14 REMARK 500 O LYS C 21 CB ASP C 93 1.15 REMARK 500 C1' A A 806 CE1 HIS E 123 1.19 REMARK 500 CB PHE C 69 N HIS C 70 1.21 REMARK 500 OD1 ASP C 75 OH TYR C 83 1.22 REMARK 500 O LYS C 21 CA ASP C 93 1.26 REMARK 500 OP2 G F 1604 N TYR C 26 1.27 REMARK 500 CB LYS E 130 CB PRO E 137 1.27 REMARK 500 O4' A A 806 ND1 HIS E 123 1.27 REMARK 500 C4' A A 806 NE2 HIS E 123 1.28 REMARK 500 O6 G F 1605 CG2 THR C 28 1.29 REMARK 500 CG LEU E 75 CD1 LEU E 80 1.31 REMARK 500 CA ALA E 126 CE LYS E 140 1.33 REMARK 500 CA ALA E 126 CD LYS E 140 1.33 REMARK 500 CA THR C 78 CB LYS C 82 1.34 REMARK 500 NH2 ARG E 127 CD1 TYR E 141 1.34 REMARK 500 O2' A F 1603 CA GLY C 25 1.35 REMARK 500 O6 G F 1604 CD PRO C 48 1.36 REMARK 500 C3' C A 804 OG1 THR E 148 1.36 REMARK 500 OP1 A A 807 CG2 THR E 145 1.37 REMARK 500 O ILE E 84 CB GLU E 86 1.37 REMARK 500 O4' A A 806 NE2 HIS E 123 1.39 REMARK 500 CD LYS E 130 C PRO E 137 1.39 REMARK 500 CA LYS C 21 CB ASP C 93 1.42 REMARK 500 O THR C 102 N THR C 103 1.42 REMARK 500 N LYS C 21 OD2 ASP C 93 1.42 REMARK 500 CG LYS E 130 CB PRO E 137 1.42 REMARK 500 CD1 LEU E 75 CD1 LEU E 80 1.43 REMARK 500 CB THR C 78 C LYS C 82 1.43 REMARK 500 OP1 A A 807 CB THR E 145 1.44 REMARK 500 O3' G B 668 NZ LYS E 107 1.45 REMARK 500 O THR C 78 N LYS C 82 1.47 REMARK 500 CG ASP C 75 OH TYR C 83 1.48 REMARK 500 ND2 ASN C 73 CA TYR C 83 1.49 REMARK 500 REMARK 500 THIS ENTRY HAS 182 CLOSE CONTACTS REMARK 500 REMARK 500 REMARK: NULL 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 ASN C 8 CB ASN C 8 CG 0.419 REMARK 500 GLY C 20 N GLY C 20 CA 0.146 REMARK 500 LYS C 31 CD LYS C 31 CE -0.166 REMARK 500 PRO C 49 CD PRO C 49 N 0.125 REMARK 500 ALA C 79 C CYS C 80 N -0.456 REMARK 500 LYS C 82 C TYR C 83 N 0.182 REMARK 500 SER C 90 CB SER C 90 OG -0.155 REMARK 500 ILE C 91 C LEU C 92 N -0.191 REMARK 500 ASP C 93 CB ASP C 93 CG 0.981 REMARK 500 ASP C 93 C PRO C 94 N -0.141 REMARK 500 PRO C 94 CD PRO C 94 N 0.112 REMARK 500 THR C 103 C THR C 104 N -0.369 REMARK 500 CYS D 57 CA CYS D 57 CB -0.121 REMARK 500 LYS D 64 CE LYS D 64 NZ -0.154 REMARK 500 PRO E 82 C GLU E 83 N 0.219 REMARK 500 ILE E 84 N ILE E 84 CA 0.144 REMARK 500 LYS E 133 CB LYS E 133 CG 1.265 REMARK 500 LYS E 134 CB LYS E 134 CG 0.735 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 A B 687 C2' - C3' - O3' ANGL. DEV. = 11.7 DEGREES REMARK 500 ASN C 8 CA - CB - CG ANGL. DEV. = -15.7 DEGREES REMARK 500 ASN C 8 CB - CG - OD1 ANGL. DEV. = 16.1 DEGREES REMARK 500 ASN C 8 CB - CG - ND2 ANGL. DEV. = -17.1 DEGREES REMARK 500 MET C 17 CG - SD - CE ANGL. DEV. = -10.9 DEGREES REMARK 500 SER C 35 CA - CB - OG ANGL. DEV. = -18.7 DEGREES REMARK 500 PRO C 49 CA - N - CD ANGL. DEV. = -11.9 DEGREES REMARK 500 ASN C 73 CA - C - N ANGL. DEV. = -14.1 DEGREES REMARK 500 VAL C 74 C - N - CA ANGL. DEV. = -18.1 DEGREES REMARK 500 VAL C 74 CB - CA - C ANGL. DEV. = 14.3 DEGREES REMARK 500 ALA C 79 CA - C - N ANGL. DEV. = 13.9 DEGREES REMARK 500 ALA C 79 O - C - N ANGL. DEV. = -23.8 DEGREES REMARK 500 LYS C 82 CA - C - N ANGL. DEV. = 26.9 DEGREES REMARK 500 LYS C 82 O - C - N ANGL. DEV. = -27.6 DEGREES REMARK 500 TYR C 83 C - N - CA ANGL. DEV. = 37.2 DEGREES REMARK 500 TYR C 83 CB - CA - C ANGL. DEV. = -16.7 DEGREES REMARK 500 TYR C 83 N - CA - C ANGL. DEV. = 22.7 DEGREES REMARK 500 LEU C 92 CA - CB - CG ANGL. DEV. = 17.0 DEGREES REMARK 500 LEU C 92 CB - CG - CD1 ANGL. DEV. = 16.1 DEGREES REMARK 500 LEU C 92 CB - CG - CD2 ANGL. DEV. = -21.1 DEGREES REMARK 500 ASP C 93 CA - CB - CG ANGL. DEV. = -54.2 DEGREES REMARK 500 ASP C 93 CB - CG - OD1 ANGL. DEV. = 21.5 DEGREES REMARK 500 ASP C 93 CB - CG - OD2 ANGL. DEV. = -25.0 DEGREES REMARK 500 ASP C 93 CA - C - N ANGL. DEV. = 24.2 DEGREES REMARK 500 ASP C 93 O - C - N ANGL. DEV. = -27.8 DEGREES REMARK 500 PRO C 94 C - N - CA ANGL. DEV. = 17.5 DEGREES REMARK 500 PRO C 94 CA - N - CD ANGL. DEV. = -10.7 DEGREES REMARK 500 THR C 102 O - C - N ANGL. DEV. = -55.1 DEGREES REMARK 500 THR C 103 CA - C - N ANGL. DEV. = 28.1 DEGREES REMARK 500 THR C 103 O - C - N ANGL. DEV. = -29.4 DEGREES REMARK 500 THR C 104 C - N - CA ANGL. DEV. = 42.5 DEGREES REMARK 500 ALA D 51 CB - CA - C ANGL. DEV. = 10.0 DEGREES REMARK 500 ALA D 51 O - C - N ANGL. DEV. = -15.9 DEGREES REMARK 500 ALA E 77 CB - CA - C ANGL. DEV. = -11.8 DEGREES REMARK 500 GLU E 83 CA - C - N ANGL. DEV. = 17.8 DEGREES REMARK 500 GLU E 83 O - C - N ANGL. DEV. = -14.9 DEGREES REMARK 500 TYR E 89 CB - CG - CD2 ANGL. DEV. = -3.9 DEGREES REMARK 500 PHE E 90 CB - CG - CD1 ANGL. DEV. = 5.2 DEGREES REMARK 500 ARG E 104 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG E 104 NE - CZ - NH2 ANGL. DEV. = -5.3 DEGREES REMARK 500 LYS E 133 CA - CB - CG ANGL. DEV. = -29.1 DEGREES REMARK 500 LYS E 133 CA - C - N ANGL. DEV. = 17.7 DEGREES REMARK 500 LYS E 134 CA - CB - CG ANGL. DEV. = -16.9 DEGREES REMARK 500 ALA E 146 N - CA - CB ANGL. DEV. = 8.6 DEGREES REMARK 500 SER E 147 N - CA - CB ANGL. DEV. = 10.0 DEGREES REMARK 500 SER E 147 N - CA - C ANGL. DEV. = -18.1 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 CYS C 47 118.65 5.12 REMARK 500 PRO C 48 149.12 -34.35 REMARK 500 LEU C 50 -11.13 60.07 REMARK 500 ASN C 72 -149.96 169.52 REMARK 500 VAL C 74 89.29 -57.84 REMARK 500 ALA C 79 -84.58 -49.30 REMARK 500 CYS C 80 -114.60 -7.41 REMARK 500 ASP C 96 9.82 -68.20 REMARK 500 SER C 97 -163.91 -100.52 REMARK 500 ASP C 98 8.91 -159.82 REMARK 500 SER C 101 -175.37 -54.13 REMARK 500 THR C 102 66.42 -35.49 REMARK 500 TYR D 18 -23.12 82.02 REMARK 500 PHE D 41 -74.57 -68.94 REMARK 500 ALA D 51 146.18 178.90 REMARK 500 SER D 81 -81.95 -63.92 REMARK 500 GLU E 83 144.09 177.26 REMARK 500 ARG E 104 -168.00 -101.82 REMARK 500 THR E 138 -75.38 -52.09 REMARK 500 SER E 147 -116.49 106.98 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 ALA C 79 CYS C 80 145.75 REMARK 500 LYS C 82 TYR C 83 34.90 REMARK 500 ASP C 93 PRO C 94 127.13 REMARK 500 THR C 103 THR C 104 103.53 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 G B 727 0.07 SIDE CHAIN REMARK 500 TYR D 37 0.11 SIDE CHAIN REMARK 500 TYR E 89 0.14 SIDE CHAIN REMARK 500 PHE E 90 0.08 SIDE CHAIN REMARK 500 TYR E 128 0.08 SIDE CHAIN REMARK 500 ARG E 131 0.11 SIDE CHAIN REMARK 500 TYR E 141 0.10 SIDE CHAIN 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 ASN C 73 12.04 REMARK 500 ALA C 79 25.74 REMARK 500 ASP C 93 24.87 REMARK 500 THR C 102 -51.04 REMARK 500 ALA D 51 14.70 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-1125 RELATED DB: EMDB DBREF 1YSH C 1 104 UNP Q5I7K9 Q5I7K9_WHEAT 6 109 DBREF 1YSH D 10 82 UNP Q5QM99 Q5QM99_ORYSA 13 85 DBREF 1YSH E 65 148 GB 50940531 XP_479793 65 148 DBREF 1YSH A 792 819 PDB 1YSH 1YSH 792 819 DBREF 1YSH F 1579 1612 PDB 1YSH 1YSH 1579 1612 DBREF 1YSH B 652 752 PDB 1YSH 1YSH 652 752 SEQADV 1YSH LYS C 37 UNP Q5I7K9 GLU 42 SEE REMARK 999 SEQADV 1YSH TYR C 57 UNP Q5I7K9 CYS 62 SEE REMARK 999 SEQADV 1YSH SER C 101 UNP Q5I7K9 ASN 106 SEE REMARK 999 SEQRES 1 A 28 G A U G A A G C G U G C C SEQRES 2 A 28 G A A A G G C A C G U G G SEQRES 3 A 28 A A SEQRES 1 F 34 C A A C U C C G U G G A A SEQRES 2 F 34 G C C G U A A U G G C A G SEQRES 3 F 34 G A A G C G G A SEQRES 1 B 101 U A G A C G G U G G G A G SEQRES 2 B 101 A G G G U G G U G G A A U SEQRES 3 B 101 U C C C G G A G U A G C G SEQRES 4 B 101 G U G A A A U G C G C A G SEQRES 5 B 101 A U A C C G G G A G G A A SEQRES 6 B 101 C G C C G A U G G C G A A SEQRES 7 B 101 G G C A G C C A C C U G G SEQRES 8 B 101 U C C A C C C G U G SEQRES 1 C 104 LYS ALA LYS LYS SER GLY GLU ASN ILE ASN ASN LYS LEU SEQRES 2 C 104 GLN LEU VAL MET LYS SER GLY LYS TYR THR LEU GLY TYR SEQRES 3 C 104 LYS THR VAL LEU LYS THR LEU ARG SER SER LYS GLY LYS SEQRES 4 C 104 LEU ILE ILE LEU ALA ASN ASN CYS PRO PRO LEU ARG LYS SEQRES 5 C 104 SER GLU ILE GLU TYR TYR ALA MET LEU ALA LYS ILE SER SEQRES 6 C 104 VAL HIS HIS PHE HIS GLY ASN ASN VAL ASP LEU GLY THR SEQRES 7 C 104 ALA CYS GLY LYS TYR TYR ARG VAL CYS CYS LEU SER ILE SEQRES 8 C 104 LEU ASP PRO GLY ASP SER ASP ILE ILE SER THR THR THR SEQRES 1 D 73 ILE VAL GLY LYS TYR GLY THR ARG TYR GLY ALA SER LEU SEQRES 2 D 73 ARG LYS GLN ILE LYS LYS MET GLU VAL SER GLN HIS SER SEQRES 3 D 73 LYS TYR PHE CYS GLU PHE CYS GLY LYS PHE ALA VAL LYS SEQRES 4 D 73 ARG LYS ALA VAL GLY ILE TRP GLY CYS LYS ASP CYS GLY SEQRES 5 D 73 LYS VAL LYS ALA GLY GLY ALA TYR THR MET ASN THR ALA SEQRES 6 D 73 SER ALA VAL THR VAL ARG SER THR SEQRES 1 E 84 SER VAL THR GLY SER LYS ILE LEU ARG ILE LEU LYS ALA SEQRES 2 E 84 HIS GLY LEU ALA PRO GLU ILE PRO GLU ASP LEU TYR PHE SEQRES 3 E 84 LEU ILE LYS LYS ALA VAL ALA ILE ARG LYS HIS LEU GLU SEQRES 4 E 84 ARG ASN ARG LYS ASP LYS ASP SER LYS PHE ARG LEU ILE SEQRES 5 E 84 LEU VAL GLU SER ARG ILE HIS ARG LEU ALA ARG TYR TYR SEQRES 6 E 84 LYS ARG THR LYS LYS LEU PRO PRO THR TRP LYS TYR GLU SEQRES 7 E 84 SER THR THR ALA SER THR HELIX 1 1 ILE C 9 MET C 17 1 9 HELIX 2 2 GLY C 25 SER C 35 1 11 HELIX 3 3 LEU C 50 ALA C 62 1 13 HELIX 4 4 VAL C 74 LYS C 82 1 9 HELIX 5 5 ILE D 10 GLY D 15 5 6 HELIX 6 6 GLY D 19 SER D 35 1 17 HELIX 7 7 THR D 73 THR D 82 1 10 HELIX 8 8 THR E 67 GLY E 79 1 13 HELIX 9 9 GLU E 86 LEU E 102 1 17 HELIX 10 10 LYS E 109 LYS E 133 1 25 HELIX 11 11 LEU E 135 THR E 144 1 10 SHEET 1 A 4 THR C 23 LEU C 24 0 SHEET 2 A 4 CYS C 88 ILE C 91 -1 O SER C 90 N THR C 23 SHEET 3 A 4 LEU C 40 LEU C 43 -1 N LEU C 40 O ILE C 91 SHEET 4 A 4 SER C 65 HIS C 68 1 O SER C 65 N ILE C 41 SHEET 1 B 3 VAL D 47 ALA D 51 0 SHEET 2 B 3 ILE D 54 CYS D 57 -1 O ILE D 54 N LYS D 50 SHEET 3 B 3 VAL D 63 ALA D 65 -1 O LYS D 64 N TRP D 55 SSBOND 1 CYS C 47 CYS C 87 1555 1555 2.43 SSBOND 2 CYS D 39 CYS D 57 1555 1555 1.97 SSBOND 3 CYS D 42 CYS D 60 1555 1555 2.91 CRYST1 P 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