HEADER TRANSCRIPTION 24-APR-15 4ZHE TITLE CRYSTAL STRUCTURE OF THE SEMET SUBSTITUTED TOPLESS RELATED PROTEIN 2 TITLE 2 (TPR2) N-TERMINAL DOMAIN (1-209) FROM RICE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ASPR2 PROTEIN; COMPND 3 CHAIN: A, B, C, D; COMPND 4 FRAGMENT: N-TERMINAL DOMAIN (UNP RESIDUES 1-209); COMPND 5 SYNONYM: OS01G0254100 PROTEIN, PUTATIVE CTV.2; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ORYZA SATIVA SUBSP. JAPONICA; SOURCE 3 ORGANISM_COMMON: RICE; SOURCE 4 ORGANISM_TAXID: 39947; SOURCE 5 GENE: P0705D01.10-1, ASPR2, OS01G0254100, OSJ_01134; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PSUMO KEYWDS TRANSCRIPTIONAL COREPRESSOR, ALPHA-HELICAL STRUCTURE, TETRAMERIC KEYWDS 2 PROTEIN, PLANT TRANSCRIPTIONAL REPRESSION, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR J.KE,H.MA,X.GU,J.S.BRUNZELLE,H.E.XU,K.MELCHER REVDAT 5 23-OCT-24 4ZHE 1 REMARK REVDAT 4 25-DEC-19 4ZHE 1 REMARK REVDAT 3 06-SEP-17 4ZHE 1 REMARK REVDAT 2 09-DEC-15 4ZHE 1 JRNL REVDAT 1 05-AUG-15 4ZHE 0 JRNL AUTH J.KE,H.MA,X.GU,A.THELEN,J.S.BRUNZELLE,J.LI,H.E.XU,K.MELCHER JRNL TITL STRUCTURAL BASIS FOR RECOGNITION OF DIVERSE TRANSCRIPTIONAL JRNL TITL 2 REPRESSORS BY THE TOPLESS FAMILY OF COREPRESSORS. JRNL REF SCI ADV V. 1 00107 2015 JRNL REFN ESSN 2375-2548 JRNL PMID 26601214 JRNL DOI 10.1126/SCIADV.1500107 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.28 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.410 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 40217 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.202 REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.242 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.080 REMARK 3 FREE R VALUE TEST SET COUNT : 3871 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 44.2904 - 7.5793 0.99 2551 158 0.1673 0.2087 REMARK 3 2 7.5793 - 6.0207 1.00 2600 124 0.2132 0.2569 REMARK 3 3 6.0207 - 5.2611 1.00 2589 137 0.2159 0.2438 REMARK 3 4 5.2611 - 4.7807 1.00 2576 145 0.1760 0.1977 REMARK 3 5 4.7807 - 4.4384 1.00 2578 125 0.1716 0.2099 REMARK 3 6 4.4384 - 4.1769 1.00 2601 138 0.1630 0.2172 REMARK 3 7 4.1769 - 3.9678 1.00 2572 160 0.1687 0.2005 REMARK 3 8 3.9678 - 3.7952 1.00 2602 123 0.1681 0.1927 REMARK 3 9 3.7952 - 3.6492 1.00 2564 139 0.1785 0.2038 REMARK 3 10 3.6492 - 3.5233 1.00 2581 143 0.1950 0.2531 REMARK 3 11 3.5233 - 3.4132 1.00 2598 126 0.2110 0.2641 REMARK 3 12 3.4132 - 3.3157 1.00 2569 135 0.2242 0.2934 REMARK 3 13 3.3157 - 3.2284 1.00 2617 136 0.2159 0.2473 REMARK 3 14 3.2284 - 3.1497 1.00 2522 154 0.2213 0.2852 REMARK 3 15 3.1497 - 3.0781 1.00 2625 145 0.2245 0.3175 REMARK 3 16 3.0781 - 3.0126 1.00 2563 123 0.2239 0.3581 REMARK 3 17 3.0126 - 2.9523 1.00 2626 113 0.2183 0.2607 REMARK 3 18 2.9523 - 2.8966 1.00 2559 168 0.2382 0.2821 REMARK 3 19 2.8966 - 2.8449 1.00 2571 139 0.2366 0.2598 REMARK 3 20 2.8449 - 2.7967 1.00 2620 104 0.2268 0.3265 REMARK 3 21 2.7967 - 2.7516 1.00 2615 142 0.2364 0.2605 REMARK 3 22 2.7516 - 2.7093 1.00 2541 184 0.2386 0.2683 REMARK 3 23 2.7093 - 2.6694 1.00 2607 120 0.2389 0.3190 REMARK 3 24 2.6694 - 2.6318 1.00 2590 120 0.2462 0.2844 REMARK 3 25 2.6318 - 2.5963 1.00 2523 139 0.2463 0.2878 REMARK 3 26 2.5963 - 2.5625 1.00 2641 140 0.2476 0.2775 REMARK 3 27 2.5625 - 2.5305 1.00 2541 153 0.2753 0.2680 REMARK 3 28 2.5305 - 2.5000 1.00 2599 138 0.2811 0.3181 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.290 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.410 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.012 6942 REMARK 3 ANGLE : 1.459 9320 REMARK 3 CHIRALITY : 0.065 1026 REMARK 3 PLANARITY : 0.007 1178 REMARK 3 DIHEDRAL : 14.621 2650 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4ZHE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-MAY-15. REMARK 100 THE DEPOSITION ID IS D_1000209281. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-AUG-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97872 REMARK 200 MONOCHROMATOR : NI FILTER REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 43276 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.440 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 14.80 REMARK 200 R MERGE (I) : 0.11500 REMARK 200 R SYM (I) : 0.11500 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 19.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.44 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.57 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 15.00 REMARK 200 R MERGE FOR SHELL (I) : 1.28000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: ROD SHAPED. REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.86 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% W/V PEG 3,350, 0.2 M MAGNESIUM REMARK 280 CHLORIDE, 0.1 M BIS-TRIS, PH 6.5, 19.6 MM 5-METHYL-6-O-(N- REMARK 280 HEPTYLCARBAMOYL)-ALPHA-D-GLUCOPYRANOSIDE, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 35.07450 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 72.47350 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 55.94100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 72.47350 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 35.07450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 55.94100 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 PRO A 206 REMARK 465 PRO A 207 REMARK 465 ASN A 208 REMARK 465 GLY A 209 REMARK 465 PRO B 191 REMARK 465 ASN B 192 REMARK 465 PRO B 193 REMARK 465 ASP B 194 REMARK 465 ASN B 208 REMARK 465 GLY B 209 REMARK 465 PRO C 189 REMARK 465 ARG C 190 REMARK 465 PRO C 191 REMARK 465 ASN C 192 REMARK 465 PRO C 193 REMARK 465 ASP C 194 REMARK 465 ILE C 195 REMARK 465 PRO C 207 REMARK 465 ASN C 208 REMARK 465 GLY C 209 REMARK 465 PRO D 207 REMARK 465 ASN D 208 REMARK 465 GLY D 209 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 LYS A 187 CG CD CE NZ REMARK 470 ASN A 188 CG OD1 ND2 REMARK 470 ASN A 192 CG OD1 ND2 REMARK 470 THR A 205 OG1 CG2 REMARK 470 LYS B 196 CG CD CE NZ REMARK 470 GLN C 184 CG CD OE1 NE2 REMARK 470 LYS D 132 CG CD CE NZ REMARK 470 GLN D 182 CG CD OE1 NE2 REMARK 470 HIS D 183 CG ND1 CD2 CE1 NE2 REMARK 470 CYS D 186 SG REMARK 470 LYS D 187 CG CD CE NZ REMARK 470 ARG D 190 CG CD NE CZ NH1 NH2 REMARK 470 ASN D 192 CG OD1 ND2 REMARK 470 ILE D 195 CG1 CG2 CD1 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O SER A 131 OG SER B 141 4566 2.18 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 GLU B 128 CB GLU B 128 CG -0.213 REMARK 500 GLU B 128 CG GLU B 128 CD -0.198 REMARK 500 GLU B 128 CD GLU B 128 OE1 -0.108 REMARK 500 LYS B 149 CE LYS B 149 NZ -0.158 REMARK 500 ARG C 67 CZ ARG C 67 NH2 -0.090 REMARK 500 GLU C 159 CG GLU C 159 CD -0.137 REMARK 500 LEU D 185 CA LEU D 185 CB 0.144 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 ARG C 90 CD - NE - CZ ANGL. DEV. = -9.9 DEGREES REMARK 500 ARG C 90 NE - CZ - NH1 ANGL. DEV. = -10.7 DEGREES REMARK 500 ARG C 90 NE - CZ - NH2 ANGL. DEV. = 11.2 DEGREES REMARK 500 LEU C 185 N - CA - C ANGL. DEV. = -16.2 DEGREES REMARK 500 CYS C 186 CA - CB - SG ANGL. DEV. = 8.9 DEGREES REMARK 500 CYS D 186 N - CA - CB ANGL. DEV. = 12.6 DEGREES REMARK 500 PRO D 191 C - N - CA ANGL. DEV. = -10.5 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 SER A 2 -72.79 -129.26 REMARK 500 LYS A 187 -170.43 -67.23 REMARK 500 PRO A 189 78.57 -67.90 REMARK 500 CYS A 204 -58.16 -122.38 REMARK 500 LYS D 196 -71.24 -81.49 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B 434 DISTANCE = 6.39 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5C6Q RELATED DB: PDB REMARK 900 RELATED ID: 5C6V RELATED DB: PDB REMARK 900 RELATED ID: 5C7E RELATED DB: PDB REMARK 900 RELATED ID: 5C7F RELATED DB: PDB DBREF 4ZHE A 1 209 UNP Q5NBT9 Q5NBT9_ORYSJ 1 209 DBREF 4ZHE B 1 209 UNP Q5NBT9 Q5NBT9_ORYSJ 1 209 DBREF 4ZHE C 1 209 UNP Q5NBT9 Q5NBT9_ORYSJ 1 209 DBREF 4ZHE D 1 209 UNP Q5NBT9 Q5NBT9_ORYSJ 1 209 SEQRES 1 A 209 MSE SER SER LEU SER ARG GLU LEU VAL PHE LEU ILE LEU SEQRES 2 A 209 GLN PHE LEU ASP GLU GLU LYS PHE LYS GLU THR VAL HIS SEQRES 3 A 209 LYS LEU GLU GLN GLU SER GLY PHE PHE PHE ASN MSE LYS SEQRES 4 A 209 TYR PHE GLU GLU LYS VAL HIS ALA GLY GLU TRP ASP GLU SEQRES 5 A 209 VAL GLU LYS TYR LEU SER GLY PHE THR LYS VAL ASP ASP SEQRES 6 A 209 ASN ARG TYR SER MSE LYS ILE PHE PHE GLU ILE ARG LYS SEQRES 7 A 209 GLN LYS TYR LEU GLU ALA LEU ASP ARG HIS ASP ARG ALA SEQRES 8 A 209 LYS ALA VAL ASP ILE LEU VAL LYS ASP LEU LYS VAL PHE SEQRES 9 A 209 SER THR PHE ASN GLU GLU LEU TYR LYS GLU ILE THR GLN SEQRES 10 A 209 LEU LEU THR LEU GLU ASN PHE ARG GLU ASN GLU GLN LEU SEQRES 11 A 209 SER LYS TYR GLY ASP THR LYS SER ALA ARG SER ILE MSE SEQRES 12 A 209 LEU ILE GLU LEU LYS LYS LEU ILE GLU ALA ASN PRO LEU SEQRES 13 A 209 PHE ARG GLU LYS LEU VAL PHE PRO THR LEU LYS ALA SER SEQRES 14 A 209 ARG LEU ARG THR LEU ILE ASN GLN SER LEU ASN TRP GLN SEQRES 15 A 209 HIS GLN LEU CYS LYS ASN PRO ARG PRO ASN PRO ASP ILE SEQRES 16 A 209 LYS THR LEU PHE THR ASP HIS THR CYS THR PRO PRO ASN SEQRES 17 A 209 GLY SEQRES 1 B 209 MSE SER SER LEU SER ARG GLU LEU VAL PHE LEU ILE LEU SEQRES 2 B 209 GLN PHE LEU ASP GLU GLU LYS PHE LYS GLU THR VAL HIS SEQRES 3 B 209 LYS LEU GLU GLN GLU SER GLY PHE PHE PHE ASN MSE LYS SEQRES 4 B 209 TYR PHE GLU GLU LYS VAL HIS ALA GLY GLU TRP ASP GLU SEQRES 5 B 209 VAL GLU LYS TYR LEU SER GLY PHE THR LYS VAL ASP ASP SEQRES 6 B 209 ASN ARG TYR SER MSE LYS ILE PHE PHE GLU ILE ARG LYS SEQRES 7 B 209 GLN LYS TYR LEU GLU ALA LEU ASP ARG HIS ASP ARG ALA SEQRES 8 B 209 LYS ALA VAL ASP ILE LEU VAL LYS ASP LEU LYS VAL PHE SEQRES 9 B 209 SER THR PHE ASN GLU GLU LEU TYR LYS GLU ILE THR GLN SEQRES 10 B 209 LEU LEU THR LEU GLU ASN PHE ARG GLU ASN GLU GLN LEU SEQRES 11 B 209 SER LYS TYR GLY ASP THR LYS SER ALA ARG SER ILE MSE SEQRES 12 B 209 LEU ILE GLU LEU LYS LYS LEU ILE GLU ALA ASN PRO LEU SEQRES 13 B 209 PHE ARG GLU LYS LEU VAL PHE PRO THR LEU LYS ALA SER SEQRES 14 B 209 ARG LEU ARG THR LEU ILE ASN GLN SER LEU ASN TRP GLN SEQRES 15 B 209 HIS GLN LEU CYS LYS ASN PRO ARG PRO ASN PRO ASP ILE SEQRES 16 B 209 LYS THR LEU PHE THR ASP HIS THR CYS THR PRO PRO ASN SEQRES 17 B 209 GLY SEQRES 1 C 209 MSE SER SER LEU SER ARG GLU LEU VAL PHE LEU ILE LEU SEQRES 2 C 209 GLN PHE LEU ASP GLU GLU LYS PHE LYS GLU THR VAL HIS SEQRES 3 C 209 LYS LEU GLU GLN GLU SER GLY PHE PHE PHE ASN MSE LYS SEQRES 4 C 209 TYR PHE GLU GLU LYS VAL HIS ALA GLY GLU TRP ASP GLU SEQRES 5 C 209 VAL GLU LYS TYR LEU SER GLY PHE THR LYS VAL ASP ASP SEQRES 6 C 209 ASN ARG TYR SER MSE LYS ILE PHE PHE GLU ILE ARG LYS SEQRES 7 C 209 GLN LYS TYR LEU GLU ALA LEU ASP ARG HIS ASP ARG ALA SEQRES 8 C 209 LYS ALA VAL ASP ILE LEU VAL LYS ASP LEU LYS VAL PHE SEQRES 9 C 209 SER THR PHE ASN GLU GLU LEU TYR LYS GLU ILE THR GLN SEQRES 10 C 209 LEU LEU THR LEU GLU ASN PHE ARG GLU ASN GLU GLN LEU SEQRES 11 C 209 SER LYS TYR GLY ASP THR LYS SER ALA ARG SER ILE MSE SEQRES 12 C 209 LEU ILE GLU LEU LYS LYS LEU ILE GLU ALA ASN PRO LEU SEQRES 13 C 209 PHE ARG GLU LYS LEU VAL PHE PRO THR LEU LYS ALA SER SEQRES 14 C 209 ARG LEU ARG THR LEU ILE ASN GLN SER LEU ASN TRP GLN SEQRES 15 C 209 HIS GLN LEU CYS LYS ASN PRO ARG PRO ASN PRO ASP ILE SEQRES 16 C 209 LYS THR LEU PHE THR ASP HIS THR CYS THR PRO PRO ASN SEQRES 17 C 209 GLY SEQRES 1 D 209 MSE SER SER LEU SER ARG GLU LEU VAL PHE LEU ILE LEU SEQRES 2 D 209 GLN PHE LEU ASP GLU GLU LYS PHE LYS GLU THR VAL HIS SEQRES 3 D 209 LYS LEU GLU GLN GLU SER GLY PHE PHE PHE ASN MSE LYS SEQRES 4 D 209 TYR PHE GLU GLU LYS VAL HIS ALA GLY GLU TRP ASP GLU SEQRES 5 D 209 VAL GLU LYS TYR LEU SER GLY PHE THR LYS VAL ASP ASP SEQRES 6 D 209 ASN ARG TYR SER MSE LYS ILE PHE PHE GLU ILE ARG LYS SEQRES 7 D 209 GLN LYS TYR LEU GLU ALA LEU ASP ARG HIS ASP ARG ALA SEQRES 8 D 209 LYS ALA VAL ASP ILE LEU VAL LYS ASP LEU LYS VAL PHE SEQRES 9 D 209 SER THR PHE ASN GLU GLU LEU TYR LYS GLU ILE THR GLN SEQRES 10 D 209 LEU LEU THR LEU GLU ASN PHE ARG GLU ASN GLU GLN LEU SEQRES 11 D 209 SER LYS TYR GLY ASP THR LYS SER ALA ARG SER ILE MSE SEQRES 12 D 209 LEU ILE GLU LEU LYS LYS LEU ILE GLU ALA ASN PRO LEU SEQRES 13 D 209 PHE ARG GLU LYS LEU VAL PHE PRO THR LEU LYS ALA SER SEQRES 14 D 209 ARG LEU ARG THR LEU ILE ASN GLN SER LEU ASN TRP GLN SEQRES 15 D 209 HIS GLN LEU CYS LYS ASN PRO ARG PRO ASN PRO ASP ILE SEQRES 16 D 209 LYS THR LEU PHE THR ASP HIS THR CYS THR PRO PRO ASN SEQRES 17 D 209 GLY MODRES 4ZHE MSE A 1 MET MODIFIED RESIDUE MODRES 4ZHE MSE A 38 MET MODIFIED RESIDUE MODRES 4ZHE MSE A 70 MET MODIFIED RESIDUE MODRES 4ZHE MSE A 143 MET MODIFIED RESIDUE MODRES 4ZHE MSE B 1 MET MODIFIED RESIDUE MODRES 4ZHE MSE B 38 MET MODIFIED RESIDUE MODRES 4ZHE MSE B 70 MET MODIFIED RESIDUE MODRES 4ZHE MSE B 143 MET MODIFIED RESIDUE MODRES 4ZHE MSE C 1 MET MODIFIED RESIDUE MODRES 4ZHE MSE C 38 MET MODIFIED RESIDUE MODRES 4ZHE MSE C 70 MET MODIFIED RESIDUE MODRES 4ZHE MSE C 143 MET MODIFIED RESIDUE MODRES 4ZHE MSE D 1 MET MODIFIED RESIDUE MODRES 4ZHE MSE D 38 MET MODIFIED RESIDUE MODRES 4ZHE MSE D 70 MET MODIFIED RESIDUE MODRES 4ZHE MSE D 143 MET MODIFIED RESIDUE HET MSE A 1 8 HET MSE A 38 8 HET MSE A 70 8 HET MSE A 143 8 HET MSE B 1 8 HET MSE B 38 8 HET MSE B 70 8 HET MSE B 143 8 HET MSE C 1 8 HET MSE C 38 8 HET MSE C 70 8 HET MSE C 143 8 HET MSE D 1 8 HET MSE D 38 8 HET MSE D 70 8 HET MSE D 143 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 16(C5 H11 N O2 SE) FORMUL 5 HOH *378(H2 O) HELIX 1 AA1 SER A 2 GLU A 19 1 18 HELIX 2 AA2 PHE A 21 GLY A 33 1 13 HELIX 3 AA3 ASN A 37 ALA A 47 1 11 HELIX 4 AA4 GLU A 49 SER A 58 1 10 HELIX 5 AA5 ASN A 66 ARG A 87 1 22 HELIX 6 AA6 ASP A 89 ASP A 100 1 12 HELIX 7 AA7 LEU A 101 SER A 105 5 5 HELIX 8 AA8 ASN A 108 LEU A 118 1 11 HELIX 9 AA9 LEU A 119 LEU A 121 5 3 HELIX 10 AB1 ASN A 123 SER A 131 5 9 HELIX 11 AB2 ASP A 135 ASN A 154 1 20 HELIX 12 AB3 PRO A 155 ARG A 158 5 4 HELIX 13 AB4 SER A 169 LEU A 185 1 17 HELIX 14 AB5 SER B 2 GLU B 19 1 18 HELIX 15 AB6 PHE B 21 GLY B 33 1 13 HELIX 16 AB7 ASN B 37 ALA B 47 1 11 HELIX 17 AB8 GLU B 49 SER B 58 1 10 HELIX 18 AB9 ASN B 66 ARG B 87 1 22 HELIX 19 AC1 ASP B 89 ASP B 100 1 12 HELIX 20 AC2 LEU B 101 SER B 105 5 5 HELIX 21 AC3 ASN B 108 LEU B 118 1 11 HELIX 22 AC4 LEU B 119 LEU B 121 5 3 HELIX 23 AC5 ASN B 123 SER B 131 5 9 HELIX 24 AC6 ASP B 135 ASN B 154 1 20 HELIX 25 AC7 SER B 169 HIS B 183 1 15 HELIX 26 AC8 SER C 2 GLU C 19 1 18 HELIX 27 AC9 PHE C 21 GLY C 33 1 13 HELIX 28 AD1 ASN C 37 ALA C 47 1 11 HELIX 29 AD2 GLU C 49 SER C 58 1 10 HELIX 30 AD3 ASN C 66 ARG C 87 1 22 HELIX 31 AD4 ASP C 89 ASP C 100 1 12 HELIX 32 AD5 LEU C 101 SER C 105 5 5 HELIX 33 AD6 ASN C 108 LEU C 118 1 11 HELIX 34 AD7 LEU C 119 LEU C 121 5 3 HELIX 35 AD8 ASN C 123 SER C 131 5 9 HELIX 36 AD9 ASP C 135 ASN C 154 1 20 HELIX 37 AE1 PRO C 155 ARG C 158 5 4 HELIX 38 AE2 SER C 169 HIS C 183 1 15 HELIX 39 AE3 SER D 2 GLU D 19 1 18 HELIX 40 AE4 PHE D 21 GLY D 33 1 13 HELIX 41 AE5 ASN D 37 ALA D 47 1 11 HELIX 42 AE6 GLU D 49 SER D 58 1 10 HELIX 43 AE7 ASN D 66 ARG D 87 1 22 HELIX 44 AE8 ASP D 89 ASP D 100 1 12 HELIX 45 AE9 LEU D 101 SER D 105 5 5 HELIX 46 AF1 ASN D 108 LEU D 118 1 11 HELIX 47 AF2 LEU D 119 LEU D 121 5 3 HELIX 48 AF3 ASN D 123 SER D 131 5 9 HELIX 49 AF4 ASP D 135 ASN D 154 1 20 HELIX 50 AF5 PRO D 155 ARG D 158 5 4 HELIX 51 AF6 SER D 169 GLN D 184 1 16 SSBOND 1 CYS A 186 CYS A 204 1555 1555 2.03 SSBOND 2 CYS B 186 CYS B 204 1555 1555 2.06 LINK C MSE A 1 N SER A 2 1555 1555 1.33 LINK C ASN A 37 N MSE A 38 1555 1555 1.33 LINK C MSE A 38 N LYS A 39 1555 1555 1.32 LINK C SER A 69 N MSE A 70 1555 1555 1.32 LINK C MSE A 70 N LYS A 71 1555 1555 1.32 LINK C ILE A 142 N MSE A 143 1555 1555 1.32 LINK C MSE A 143 N LEU A 144 1555 1555 1.32 LINK C MSE B 1 N SER B 2 1555 1555 1.32 LINK C ASN B 37 N MSE B 38 1555 1555 1.33 LINK C MSE B 38 N LYS B 39 1555 1555 1.32 LINK C SER B 69 N MSE B 70 1555 1555 1.33 LINK C MSE B 70 N LYS B 71 1555 1555 1.33 LINK C ILE B 142 N MSE B 143 1555 1555 1.33 LINK C MSE B 143 N LEU B 144 1555 1555 1.33 LINK C MSE C 1 N SER C 2 1555 1555 1.33 LINK C ASN C 37 N MSE C 38 1555 1555 1.33 LINK C MSE C 38 N LYS C 39 1555 1555 1.32 LINK C SER C 69 N MSE C 70 1555 1555 1.33 LINK C MSE C 70 N LYS C 71 1555 1555 1.33 LINK C ILE C 142 N MSE C 143 1555 1555 1.33 LINK C MSE C 143 N LEU C 144 1555 1555 1.33 LINK C MSE D 1 N SER D 2 1555 1555 1.32 LINK C ASN D 37 N MSE D 38 1555 1555 1.33 LINK C MSE D 38 N LYS D 39 1555 1555 1.33 LINK C SER D 69 N MSE D 70 1555 1555 1.32 LINK C MSE D 70 N LYS D 71 1555 1555 1.32 LINK C ILE D 142 N MSE D 143 1555 1555 1.32 LINK C MSE D 143 N LEU D 144 1555 1555 1.33 CISPEP 1 PRO A 191 ASN A 192 0 2.48 CISPEP 2 ASN A 192 PRO A 193 0 -9.96 CISPEP 3 CYS D 186 LYS D 187 0 -9.59 CRYST1 70.149 111.882 144.947 90.00 90.00 90.00 P 21 21 21 16 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 0.014255 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008938 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006899 0.00000 MTRIX1 1 1.000000 0.000000 0.000000 0.00000 1 MTRIX2 1 0.000000 1.000000 0.000000 0.00000 1 MTRIX3 1 0.000000 0.000000 1.000000 0.00000 1 MTRIX1 2 -0.998117 -0.059449 0.015136 144.17496 1 MTRIX2 2 -0.057540 0.992806 0.105004 -3.28844 1 MTRIX3 2 -0.021269 0.103935 -0.994357 151.92398 1 MTRIX1 3 0.956945 0.036661 0.287945 -22.73504 1 MTRIX2 3 0.034421 -0.999325 0.012841 129.01103 1 MTRIX3 3 0.288222 -0.002377 -0.957561 133.67032 1 MTRIX1 4 -0.952287 0.008421 -0.305089 161.32710 1 MTRIX2 4 0.027886 -0.993037 -0.114452 139.50212 1 MTRIX3 4 -0.303928 -0.117499 0.945421 33.99967 1 HETATM 1 N MSE A 1 55.339 73.590 128.434 1.00140.39 N HETATM 2 CA MSE A 1 54.342 73.638 127.370 1.00139.11 C HETATM 3 C MSE A 1 54.497 74.921 126.582 1.00133.81 C HETATM 4 O MSE A 1 53.979 75.047 125.489 1.00133.11 O HETATM 5 CB MSE A 1 52.934 73.511 127.947 1.00144.86 C HETATM 6 CG MSE A 1 52.585 74.579 128.951 1.00154.89 C HETATM 7 SE MSE A 1 51.925 73.786 130.588 0.55175.18 SE HETATM 8 CE MSE A 1 53.357 74.273 131.795 1.00165.05 C