HEADER PLANT PROTEIN 23-NOV-20 7DK8 TITLE CRYSTAL STRUCTURE OF OSGH3-8 WITH AMP COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROBABLE INDOLE-3-ACETIC ACID-AMIDO SYNTHETASE GH3.8; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: AUXIN-RESPONSIVE GH3-LIKE PROTEIN 8,OSGH3-8; COMPND 5 EC: 6.3.2.-; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ORYZA SATIVA SUBSP. INDICA; SOURCE 3 ORGANISM_COMMON: RICE; SOURCE 4 ORGANISM_TAXID: 39946; SOURCE 5 GENE: GH3.8, OSI_025789; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 866768 KEYWDS ACYL ACID AMIDO SYNTHETASES, AUXIN, ACTIVE SITE, PLANT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Y.K.ZHANG,G.L.XU,Z.H.MING REVDAT 3 29-NOV-23 7DK8 1 REMARK REVDAT 2 20-JAN-21 7DK8 1 JRNL REVDAT 1 23-DEC-20 7DK8 0 JRNL AUTH G.XU,Y.ZHANG,M.LI,X.JIAO,L.ZHOU,Z.MING JRNL TITL CRYSTAL STRUCTURE OF THE ACYL ACID AMIDO SYNTHETASE GH3-8 JRNL TITL 2 FROM ORYZA SATIVA. JRNL REF BIOCHEM.BIOPHYS.RES.COMMUN. V. 534 266 2021 JRNL REFN ESSN 1090-2104 JRNL PMID 33272567 JRNL DOI 10.1016/J.BBRC.2020.11.098 REMARK 2 REMARK 2 RESOLUTION. 1.99 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.15_3459 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) : 1.99 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.58 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 3 NUMBER OF REFLECTIONS : 35491 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.200 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.256 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.510 REMARK 3 FREE R VALUE TEST SET COUNT : 1955 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 24.5700 - 4.7856 1.00 2509 143 0.1746 0.2125 REMARK 3 2 4.7856 - 3.8030 1.00 2455 151 0.1622 0.2429 REMARK 3 3 3.8030 - 3.3236 1.00 2432 147 0.1868 0.2435 REMARK 3 4 3.3236 - 3.0203 1.00 2424 141 0.2144 0.2499 REMARK 3 5 3.0203 - 2.8042 1.00 2445 145 0.2296 0.2823 REMARK 3 6 2.8042 - 2.6390 0.99 2419 135 0.2241 0.2831 REMARK 3 7 2.6390 - 2.5070 0.99 2385 142 0.2266 0.3055 REMARK 3 8 2.5070 - 2.3980 0.99 2387 134 0.2302 0.2853 REMARK 3 9 2.3980 - 2.3057 0.98 2368 135 0.2230 0.3167 REMARK 3 10 2.3057 - 2.2262 0.98 2387 139 0.2233 0.2682 REMARK 3 11 2.2262 - 2.1567 0.97 2341 132 0.2422 0.3451 REMARK 3 12 2.1567 - 2.0950 0.97 2343 135 0.2419 0.3012 REMARK 3 13 2.0950 - 2.0399 0.96 2344 138 0.2543 0.3267 REMARK 3 14 2.0399 - 1.9902 0.96 2297 138 0.2703 0.3367 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) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.760 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 47.57 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 7DK8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 02-DEC-20. REMARK 100 THE DEPOSITION ID IS D_1300019562. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-JAN-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979183 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35491 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.990 REMARK 200 RESOLUTION RANGE LOW (A) : 30.520 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 200 DATA REDUNDANCY : 19.80 REMARK 200 R MERGE (I) : 0.02218 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.99 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.04 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.30720 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 4B2G REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.52 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.08M TRIS PH 8.0, 0.1M TRIS-HCL (PH REMARK 280 8.5), 22.4% (W/V) PEG 4000, 0.02M BIS-TRIS PH 6.5, 5% (W/V) PEG REMARK 280 3350, 0.2 MICROLITER 275.0MM 2,6-DIMETHYL-4-HEPTYL-BETA-D- REMARK 280 MALTOPYRANOSIDE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-Y,X,Z+1/2 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 31.33500 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 31.33500 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 31.33500 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 660 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22670 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -3.0 KCAL/MOL 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 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 ASP A 1 REMARK 465 VAL A 2 REMARK 465 SER A 3 REMARK 465 THR A 4 REMARK 465 THR A 5 REMARK 465 GLY A 6 REMARK 465 THR A 7 REMARK 465 ALA A 8 REMARK 465 LEU A 9 REMARK 465 ARG A 10 REMARK 465 THR A 11 REMARK 465 PRO A 12 REMARK 465 ALA A 13 REMARK 465 ALA A 14 REMARK 465 GLY A 15 REMARK 465 ALA A 16 REMARK 465 VAL A 17 REMARK 465 LYS A 18 REMARK 465 GLU A 19 REMARK 465 GLY A 20 REMARK 465 ASP A 21 REMARK 465 VAL A 22 REMARK 465 TYR A 189 REMARK 465 ASP A 375 REMARK 465 GLU A 376 REMARK 465 THR A 377 REMARK 465 GLY A 378 REMARK 465 ALA A 379 REMARK 465 ALA A 380 REMARK 465 SER A 381 REMARK 465 GLY A 382 REMARK 465 LYS A 495 REMARK 465 GLY A 496 REMARK 465 ALA A 497 REMARK 465 GLY A 498 REMARK 465 ALA A 499 REMARK 465 THR A 500 REMARK 465 ALA A 596 REMARK 465 ARG A 597 REMARK 465 ARG A 598 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 ARG A 187 CG CD NE CZ NH1 NH2 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 OG SER A 234 OE1 GLU A 443 1.83 REMARK 500 O HOH A 881 O HOH A 882 1.91 REMARK 500 NH2 ARG A 541 O HOH A 701 1.93 REMARK 500 O GLU A 443 O HOH A 702 1.94 REMARK 500 OD2 ASP A 383 OG1 THR A 385 1.95 REMARK 500 O HOH A 873 O HOH A 874 1.96 REMARK 500 O SER A 554 O HOH A 703 1.98 REMARK 500 O HOH A 788 O HOH A 796 2.02 REMARK 500 NH1 ARG A 129 O HOH A 704 2.07 REMARK 500 O PRO A 373 O HOH A 705 2.08 REMARK 500 O HOH A 811 O HOH A 863 2.09 REMARK 500 OE2 GLU A 547 O HOH A 706 2.12 REMARK 500 NH1 ARG A 241 O ILE A 482 2.13 REMARK 500 OE2 GLU A 162 NZ LYS A 180 2.14 REMARK 500 O ILE A 553 N ARG A 555 2.16 REMARK 500 NH1 ARG A 238 OE2 GLU A 443 2.17 REMARK 500 REMARK 500 REMARK: NULL 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 PRO A 102 NH2 ARG A 541 6554 1.88 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 PRO A 102 C - N - CD ANGL. DEV. = -17.2 DEGREES REMARK 500 ARG A 541 NE - CZ - NH2 ANGL. DEV. = 5.2 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 LYS A 150 30.66 -90.15 REMARK 500 HIS A 183 -38.38 -38.93 REMARK 500 ASN A 186 73.40 -102.24 REMARK 500 ASP A 265 108.82 -35.49 REMARK 500 CYS A 343 129.83 -176.72 REMARK 500 ARG A 411 53.03 39.32 REMARK 500 ASN A 425 -130.08 55.13 REMARK 500 VAL A 433 -62.90 -96.53 REMARK 500 GLU A 443 -114.82 -142.86 REMARK 500 SER A 554 65.22 -51.20 REMARK 500 ARG A 555 -72.48 140.90 REMARK 500 THR A 569 89.16 -48.83 REMARK 500 PRO A 571 -78.02 -93.91 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 THR A 569 PHE A 570 -143.20 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 A 882 DISTANCE = 5.82 ANGSTROMS REMARK 525 HOH A 883 DISTANCE = 5.84 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue AMP A 601 DBREF 7DK8 A 1 598 UNP A3BLS0 GH38_ORYSI 6 603 SEQRES 1 A 598 ASP VAL SER THR THR GLY THR ALA LEU ARG THR PRO ALA SEQRES 2 A 598 ALA GLY ALA VAL LYS GLU GLY ASP VAL GLU LYS LEU ARG SEQRES 3 A 598 PHE ILE ASP GLU MET THR THR ASN VAL ASP ALA VAL GLN SEQRES 4 A 598 GLU ARG VAL LEU GLY GLU ILE LEU GLY ARG ASN ALA GLY SEQRES 5 A 598 THR GLU TYR LEU THR LYS CYS GLY LEU ASP GLY ALA THR SEQRES 6 A 598 ASP ARG ALA ALA PHE ARG ALA LYS VAL PRO VAL VAL SER SEQRES 7 A 598 TYR ASP ASP LEU GLN PRO TYR ILE GLN ARG ILE ALA ASN SEQRES 8 A 598 GLY ASP ARG SER PRO ILE LEU SER THR HIS PRO VAL SER SEQRES 9 A 598 GLU PHE LEU THR SER SER GLY THR SER ALA GLY GLU ARG SEQRES 10 A 598 LYS LEU MET PRO THR ILE MET ASP GLU LEU ASP ARG ARG SEQRES 11 A 598 GLN LEU LEU TYR SER LEU LEU MET PRO VAL MET ASN LEU SEQRES 12 A 598 TYR VAL PRO GLY LEU ASP LYS GLY LYS GLY LEU TYR PHE SEQRES 13 A 598 LEU PHE VAL LYS SER GLU THR LYS THR PRO GLY GLY LEU SEQRES 14 A 598 THR ALA ARG PRO VAL LEU THR SER TYR TYR LYS SER ASP SEQRES 15 A 598 HIS PHE LYS ASN ARG PRO TYR ASP PRO TYR HIS ASN TYR SEQRES 16 A 598 THR SER PRO THR ALA ALA ILE LEU CYS ALA ASP ALA PHE SEQRES 17 A 598 GLN SER MET TYR ALA GLN MET VAL CYS GLY LEU CYS GLN SEQRES 18 A 598 ARG ASN ASP VAL LEU ARG LEU GLY ALA VAL PHE ALA SER SEQRES 19 A 598 GLY LEU LEU ARG ALA ILE ARG PHE LEU GLN LEU ASN TRP SEQRES 20 A 598 GLU GLN LEU ALA ASP ASP ILE GLU SER GLY GLU LEU THR SEQRES 21 A 598 PRO ARG VAL THR ASP PRO SER VAL ARG GLU ALA VAL ALA SEQRES 22 A 598 ALA ILE LEU LEU PRO ASP PRO GLU LEU ALA LYS LEU ILE SEQRES 23 A 598 ARG ALA GLU CYS SER LYS GLY ASP TRP ALA GLY ILE ILE SEQRES 24 A 598 THR ARG VAL TRP PRO ASN THR LYS TYR LEU ASP VAL ILE SEQRES 25 A 598 VAL THR GLY ALA MET ALA GLN TYR ILE PRO THR LEU GLU SEQRES 26 A 598 PHE TYR SER GLY GLY LEU PRO MET ALA CYS THR MET TYR SEQRES 27 A 598 ALA SER SER GLU CYS TYR PHE GLY LEU ASN LEU ARG PRO SEQRES 28 A 598 MET CYS ASP PRO SER GLU VAL SER TYR THR ILE MET PRO SEQRES 29 A 598 ASN MET GLY TYR PHE GLU PHE LEU PRO VAL ASP GLU THR SEQRES 30 A 598 GLY ALA ALA SER GLY ASP ALA THR GLN LEU VAL ASP LEU SEQRES 31 A 598 ALA ARG VAL GLU VAL GLY ARG GLU TYR GLU LEU VAL ILE SEQRES 32 A 598 THR THR TYR ALA GLY LEU ASN ARG TYR ARG VAL GLY ASP SEQRES 33 A 598 VAL LEU ARG VAL THR GLY PHE HIS ASN ALA ALA PRO GLN SEQRES 34 A 598 PHE ARG PHE VAL ARG ARG LYS ASN VAL LEU LEU SER ILE SEQRES 35 A 598 GLU SER ASP LYS THR ASP GLU ALA GLU LEU GLN ARG ALA SEQRES 36 A 598 VAL GLU ARG ALA SER ALA LEU LEU ARG PRO HIS GLY ALA SEQRES 37 A 598 SER VAL VAL GLU TYR THR SER GLN ALA CYS THR LYS ARG SEQRES 38 A 598 ILE PRO GLY HIS TYR VAL ILE TYR TRP GLU LEU LEU THR SEQRES 39 A 598 LYS GLY ALA GLY ALA THR VAL VAL ASP ALA ASP THR LEU SEQRES 40 A 598 GLY ARG CYS CYS LEU GLU MET GLU GLU ALA LEU ASN THR SEQRES 41 A 598 VAL TYR ARG GLN SER ARG VAL ALA ASP GLY SER ILE GLY SEQRES 42 A 598 PRO LEU GLU ILE ARG VAL VAL ARG PRO GLY THR PHE GLU SEQRES 43 A 598 GLU LEU MET ASP TYR ALA ILE SER ARG GLY ALA SER ILE SEQRES 44 A 598 ASN GLN TYR LYS VAL PRO ARG CYS VAL THR PHE PRO PRO SEQRES 45 A 598 ILE VAL GLU LEU LEU ASP SER ARG VAL VAL SER SER HIS SEQRES 46 A 598 PHE SER PRO ALA LEU PRO HIS TRP THR PRO ALA ARG ARG HET AMP A 601 35 HETNAM AMP ADENOSINE MONOPHOSPHATE FORMUL 2 AMP C10 H14 N5 O7 P FORMUL 3 HOH *183(H2 O) HELIX 1 AA1 GLU A 23 ASN A 34 1 12 HELIX 2 AA2 ASN A 34 ALA A 51 1 18 HELIX 3 AA3 THR A 53 CYS A 59 1 7 HELIX 4 AA4 ASP A 66 VAL A 74 1 9 HELIX 5 AA5 SER A 78 ASN A 91 1 14 HELIX 6 AA6 ILE A 123 ASN A 142 1 20 HELIX 7 AA7 GLY A 147 GLY A 151 5 5 HELIX 8 AA8 PRO A 173 LYS A 180 1 8 HELIX 9 AA9 ASP A 190 ASN A 194 5 5 HELIX 10 AB1 PRO A 198 LEU A 203 1 6 HELIX 11 AB2 ASP A 206 GLN A 221 1 16 HELIX 12 AB3 ALA A 233 GLY A 257 1 25 HELIX 13 AB4 ASP A 265 ALA A 273 1 9 HELIX 14 AB5 ASP A 279 SER A 291 1 13 HELIX 15 AB6 GLY A 297 TRP A 303 1 7 HELIX 16 AB7 THR A 314 GLN A 319 5 6 HELIX 17 AB8 TYR A 320 GLY A 329 1 10 HELIX 18 AB9 ASP A 354 VAL A 358 5 5 HELIX 19 AC1 ASP A 383 LEU A 387 5 5 HELIX 20 AC2 ALA A 391 VAL A 393 5 3 HELIX 21 AC3 GLU A 449 SER A 460 1 12 HELIX 22 AC4 ALA A 461 LEU A 462 5 2 HELIX 23 AC5 LEU A 463 GLY A 467 5 5 HELIX 24 AC6 ASP A 503 LEU A 518 1 16 HELIX 25 AC7 ASN A 519 ALA A 528 1 10 HELIX 26 AC8 GLY A 543 SER A 554 1 12 HELIX 27 AC9 ALA A 557 GLN A 561 5 5 HELIX 28 AD1 PRO A 571 SER A 579 1 9 SHEET 1 AA1 4 GLU A 116 THR A 122 0 SHEET 2 AA1 4 GLU A 105 SER A 113 -1 N LEU A 107 O MET A 120 SHEET 3 AA1 4 THR A 170 ARG A 172 1 O THR A 170 N PHE A 106 SHEET 4 AA1 4 THR A 163 LYS A 164 -1 N THR A 163 O ALA A 171 SHEET 1 AA2 4 LYS A 152 TYR A 155 0 SHEET 2 AA2 4 VAL A 225 PHE A 232 1 O LEU A 226 N LYS A 152 SHEET 3 AA2 4 TYR A 308 ILE A 312 1 O ASP A 310 N LEU A 228 SHEET 4 AA2 4 MET A 333 ALA A 334 1 O ALA A 334 N LEU A 309 SHEET 1 AA3 8 MET A 337 ALA A 339 0 SHEET 2 AA3 8 TYR A 344 LEU A 347 -1 O GLY A 346 N TYR A 338 SHEET 3 AA3 8 TYR A 360 ILE A 362 -1 O THR A 361 N LEU A 347 SHEET 4 AA3 8 ALA A 427 ARG A 435 -1 O PHE A 430 N TYR A 360 SHEET 5 AA3 8 TYR A 412 HIS A 424 -1 N VAL A 417 O ARG A 434 SHEET 6 AA3 8 GLU A 398 THR A 404 -1 N ILE A 403 O TYR A 412 SHEET 7 AA3 8 TYR A 368 PRO A 373 -1 N LEU A 372 O GLU A 400 SHEET 8 AA3 8 VAL A 388 ASP A 389 -1 O VAL A 388 N PHE A 371 SHEET 1 AA4 2 VAL A 438 LEU A 440 0 SHEET 2 AA4 2 THR A 447 ASP A 448 -1 O THR A 447 N LEU A 439 SHEET 1 AA5 4 SER A 469 CYS A 478 0 SHEET 2 AA5 4 HIS A 485 LEU A 493 -1 O LEU A 493 N SER A 469 SHEET 3 AA5 4 GLU A 536 VAL A 540 1 O ARG A 538 N ILE A 488 SHEET 4 AA5 4 VAL A 581 PHE A 586 -1 O VAL A 582 N VAL A 539 CISPEP 1 ILE A 482 PRO A 483 0 -4.96 SITE 1 AC1 16 SER A 110 ILE A 312 THR A 314 MET A 337 SITE 2 AC1 16 TYR A 338 ALA A 339 SER A 340 SER A 341 SITE 3 AC1 16 TYR A 360 ASP A 416 PHE A 432 ARG A 435 SITE 4 AC1 16 HOH A 728 HOH A 731 HOH A 817 HOH A 863 CRYST1 121.050 121.050 62.670 90.00 90.00 120.00 P 63 6 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 0.008261 0.004770 0.000000 0.00000 SCALE2 0.000000 0.009539 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015957 0.00000