HEADER TRANSFERASE 17-APR-15 4ZDL TITLE THE CRYSTAL STRUCTURE OF THE T325S MUTANT OF THE HUMAN HOLO SEPSECS COMPND MOL_ID: 1; COMPND 2 MOLECULE: O-PHOSPHOSERYL-TRNA(SEC) SELENIUM TRANSFERASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: LIVER-PANCREAS ANTIGEN,LP,SLA-P35,SLA/LP AUTOANTIGEN, COMPND 5 SELENOCYSTEINE SYNTHASE,SEC SYNTHASE,SELENOCYSTEINYL-TRNA(SEC) COMPND 6 SYNTHASE,SEP-TRNA:SEC-TRNA SYNTHASE,SEPSECS,SOLUBLE LIVER ANTIGEN, COMPND 7 SLA,UGA SUPPRESSOR TRNA-ASSOCIATED PROTEIN,TRNA(SER/SEC)-ASSOCIATED COMPND 8 ANTIGENIC PROTEIN; COMPND 9 EC: 2.9.1.2; COMPND 10 ENGINEERED: YES; COMPND 11 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: SEPSECS, TRNP48; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: SOLUBL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PQE-80 KEYWDS SELENOCYSTEINE, PYRIDOXAL PHOSPHATE, MUTATION, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR R.L.FRENCH,M.SIMONOVIC REVDAT 7 20-NOV-24 4ZDL 1 REMARK REVDAT 6 27-SEP-23 4ZDL 1 REMARK REVDAT 5 25-DEC-19 4ZDL 1 REMARK REVDAT 4 20-SEP-17 4ZDL 1 REMARK REVDAT 3 05-OCT-16 4ZDL 1 JRNL REVDAT 2 14-SEP-16 4ZDL 1 JRNL REVDAT 1 20-APR-16 4ZDL 0 JRNL AUTH A.K.PUPPALA,R.L.FRENCH,D.MATTHIES,U.BAXA,S.SUBRAMANIAM, JRNL AUTH 2 M.SIMONOVIC JRNL TITL STRUCTURAL BASIS FOR EARLY-ONSET NEUROLOGICAL DISORDERS JRNL TITL 2 CAUSED BY MUTATIONS IN HUMAN SELENOCYSTEINE SYNTHASE. JRNL REF SCI REP V. 6 32563 2016 JRNL REFN ESSN 2045-2322 JRNL PMID 27576344 JRNL DOI 10.1038/SREP32563 REMARK 2 REMARK 2 RESOLUTION. 2.26 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) : 2.26 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.22 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 84.5 REMARK 3 NUMBER OF REFLECTIONS : 44114 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.166 REMARK 3 R VALUE (WORKING SET) : 0.163 REMARK 3 FREE R VALUE : 0.221 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.970 REMARK 3 FREE R VALUE TEST SET COUNT : 2192 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 46.2335 - 5.6925 1.00 3282 220 0.1524 0.1842 REMARK 3 2 5.6925 - 4.5196 1.00 3241 110 0.1294 0.1976 REMARK 3 3 4.5196 - 3.9486 1.00 3076 220 0.1166 0.1629 REMARK 3 4 3.9486 - 3.5877 1.00 3164 110 0.1361 0.1927 REMARK 3 5 3.5877 - 3.3307 1.00 3045 220 0.1513 0.2395 REMARK 3 6 3.3307 - 3.1343 1.00 3160 110 0.1687 0.2342 REMARK 3 7 3.1343 - 2.9774 1.00 3095 124 0.1793 0.2612 REMARK 3 8 2.9774 - 2.8478 0.97 2948 206 0.2080 0.2705 REMARK 3 9 2.8478 - 2.7382 0.93 2918 109 0.2206 0.2934 REMARK 3 10 2.7382 - 2.6437 0.89 2669 220 0.2221 0.3056 REMARK 3 11 2.6437 - 2.5611 0.82 2529 110 0.2265 0.2292 REMARK 3 12 2.5611 - 2.4879 0.77 2369 110 0.2226 0.3248 REMARK 3 13 2.4879 - 2.4224 0.67 2035 109 0.2390 0.3435 REMARK 3 14 2.4224 - 2.3633 0.56 1694 107 0.2474 0.3023 REMARK 3 15 2.3633 - 2.3095 0.48 1545 107 0.2548 0.3060 REMARK 3 16 2.3095 - 2.2604 0.39 1152 107 0.2643 0.3097 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) : 0.300 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.120 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 39.08 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 43.95 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 : 0.008 7087 REMARK 3 ANGLE : 1.107 9643 REMARK 3 CHIRALITY : 0.040 1114 REMARK 3 PLANARITY : 0.004 1240 REMARK 3 DIHEDRAL : 13.633 2628 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 4ZDL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-APR-15. REMARK 100 THE DEPOSITION ID IS D_1000209033. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-FEB-14 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-F 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 : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 44262 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.250 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 85.0 REMARK 200 DATA REDUNDANCY : 14.20 REMARK 200 R MERGE (I) : 0.18400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.29 REMARK 200 COMPLETENESS FOR SHELL (%) : 40.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.70 REMARK 200 R MERGE FOR SHELL (I) : 0.98300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 3HL2 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.75 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.45 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.28-0.34 M LITHIUM CITRATE 16-18% REMARK 280 (W/V) PEG 3,350, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 285K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 34.00800 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 41.57550 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 34.00800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 41.57550 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 300 THE ASSEMBLY REPRESENTED IN THIS ENTRY HAS REGULAR REMARK 300 CYCLIC POINT SYMMETRY (SCHOENFLIES SYMBOL = C2). 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 TOTAL BURIED SURFACE AREA: 23160 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 56210 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -110.0 KCAL/MOL 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 83.15100 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A1186 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1232 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1385 LIES ON A SPECIAL POSITION. REMARK 375 HOH B1172 LIES ON A SPECIAL POSITION. REMARK 375 HOH B1212 LIES ON A SPECIAL POSITION. 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 MET A 1 REMARK 465 ASN A 2 REMARK 465 ARG A 3 REMARK 465 GLU A 4 REMARK 465 SER A 5 REMARK 465 PHE A 6 REMARK 465 ALA A 7 REMARK 465 ALA A 8 REMARK 465 GLY A 9 REMARK 465 GLU A 10 REMARK 465 ARG A 11 REMARK 465 LEU A 12 REMARK 465 VAL A 13 REMARK 465 SER A 14 REMARK 465 PRO A 15 REMARK 465 ALA A 16 REMARK 465 TYR A 17 REMARK 465 VAL A 18 REMARK 465 LYS A 463 REMARK 465 GLU A 464 REMARK 465 ARG A 465 REMARK 465 SER A 466 REMARK 465 LYS A 467 REMARK 465 GLU A 468 REMARK 465 SER A 469 REMARK 465 ASP A 470 REMARK 465 ASP A 471 REMARK 465 ASN A 472 REMARK 465 TYR A 473 REMARK 465 ASP A 474 REMARK 465 LYS A 475 REMARK 465 THR A 476 REMARK 465 GLU A 477 REMARK 465 ASP A 478 REMARK 465 VAL A 479 REMARK 465 ASP A 480 REMARK 465 ILE A 481 REMARK 465 GLU A 482 REMARK 465 GLU A 483 REMARK 465 MET A 484 REMARK 465 ALA A 485 REMARK 465 LEU A 486 REMARK 465 LYS A 487 REMARK 465 LEU A 488 REMARK 465 ASP A 489 REMARK 465 ASN A 490 REMARK 465 VAL A 491 REMARK 465 LEU A 492 REMARK 465 LEU A 493 REMARK 465 ASP A 494 REMARK 465 THR A 495 REMARK 465 TYR A 496 REMARK 465 GLN A 497 REMARK 465 ASP A 498 REMARK 465 ALA A 499 REMARK 465 SER A 500 REMARK 465 SER A 501 REMARK 465 MET B 1 REMARK 465 ASN B 2 REMARK 465 ARG B 3 REMARK 465 GLU B 4 REMARK 465 SER B 5 REMARK 465 PHE B 6 REMARK 465 ALA B 7 REMARK 465 ALA B 8 REMARK 465 GLY B 9 REMARK 465 GLU B 10 REMARK 465 ARG B 11 REMARK 465 LEU B 12 REMARK 465 VAL B 13 REMARK 465 SER B 14 REMARK 465 PRO B 15 REMARK 465 ALA B 16 REMARK 465 TYR B 17 REMARK 465 VAL B 18 REMARK 465 LYS B 463 REMARK 465 GLU B 464 REMARK 465 ARG B 465 REMARK 465 SER B 466 REMARK 465 LYS B 467 REMARK 465 GLU B 468 REMARK 465 SER B 469 REMARK 465 ASP B 470 REMARK 465 ASP B 471 REMARK 465 ASN B 472 REMARK 465 TYR B 473 REMARK 465 ASP B 474 REMARK 465 LYS B 475 REMARK 465 THR B 476 REMARK 465 GLU B 477 REMARK 465 ASP B 478 REMARK 465 VAL B 479 REMARK 465 ASP B 480 REMARK 465 ILE B 481 REMARK 465 GLU B 482 REMARK 465 GLU B 483 REMARK 465 MET B 484 REMARK 465 ALA B 485 REMARK 465 LEU B 486 REMARK 465 LYS B 487 REMARK 465 LEU B 488 REMARK 465 ASP B 489 REMARK 465 ASN B 490 REMARK 465 VAL B 491 REMARK 465 LEU B 492 REMARK 465 LEU B 493 REMARK 465 ASP B 494 REMARK 465 THR B 495 REMARK 465 TYR B 496 REMARK 465 GLN B 497 REMARK 465 ASP B 498 REMARK 465 ALA B 499 REMARK 465 SER B 500 REMARK 465 SER B 501 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 19 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 23 CG CD OE1 OE2 REMARK 470 GLU A 29 CG CD OE1 OE2 REMARK 470 ARG A 33 NE CZ NH1 NH2 REMARK 470 LYS A 38 CD CE NZ REMARK 470 LYS A 40 CE NZ REMARK 470 SER A 102 OG REMARK 470 LYS A 163 CE NZ REMARK 470 ARG A 271 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 308 NZ REMARK 470 LYS A 339 CE NZ REMARK 470 LYS A 353 CE NZ REMARK 470 LYS A 378 CE NZ REMARK 470 ASP A 381 CG OD1 OD2 REMARK 470 HIS A 383 CG ND1 CD2 CE1 NE2 REMARK 470 ARG A 384 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 386 CG CD CE NZ REMARK 470 ASN A 428 CG OD1 ND2 REMARK 470 LYS A 443 CE NZ REMARK 470 LYS A 452 CE NZ REMARK 470 ARG A 456 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 459 CG CD CE NZ REMARK 470 ARG B 19 CG CD NE CZ NH1 NH2 REMARK 470 GLN B 20 CG CD OE1 NE2 REMARK 470 CYS B 22 SG REMARK 470 GLU B 23 CG CD OE1 OE2 REMARK 470 ARG B 26 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 33 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 38 CE NZ REMARK 470 LYS B 40 CE NZ REMARK 470 LYS B 116 CE NZ REMARK 470 LYS B 158 NZ REMARK 470 LYS B 161 CE NZ REMARK 470 LYS B 163 CG CD CE NZ REMARK 470 LYS B 203 CG CD CE NZ REMARK 470 LYS B 261 CG CD CE NZ REMARK 470 GLN B 304 CD OE1 NE2 REMARK 470 LYS B 308 NZ REMARK 470 LYS B 342 CE NZ REMARK 470 GLU B 357 CG CD OE1 OE2 REMARK 470 LYS B 378 CD CE NZ REMARK 470 ASP B 381 CG OD1 OD2 REMARK 470 GLN B 390 CG CD OE1 NE2 REMARK 470 GLN B 399 CG CD OE1 NE2 REMARK 470 LYS B 443 CG CD CE NZ REMARK 470 GLN B 445 OE1 NE2 REMARK 470 LYS B 452 CG CD CE NZ REMARK 470 ARG B 456 NE CZ NH1 NH2 REMARK 470 ARG B 462 CG CD NE CZ NH1 NH2 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 OG SER A 98 OG1 FLC A 1002 2565 2.10 REMARK 500 O HOH A 1210 O HOH A 1289 2565 2.17 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 ALA A 387 N - CA - CB ANGL. DEV. = 8.6 DEGREES REMARK 500 ASP B 100 CB - CG - OD1 ANGL. DEV. = 6.1 DEGREES REMARK 500 PRO B 160 C - N - CA ANGL. DEV. = 9.6 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 VAL A 131 73.16 -104.16 REMARK 500 PRO A 141 45.72 -78.52 REMARK 500 THR A 224 -79.33 -89.19 REMARK 500 ALA A 387 -41.75 -134.14 REMARK 500 MET A 423 2.41 84.78 REMARK 500 GLN B 20 4.83 -68.89 REMARK 500 ALA B 108 62.47 -152.22 REMARK 500 VAL B 131 76.30 -108.20 REMARK 500 PRO B 141 43.04 -72.09 REMARK 500 THR B 224 -76.42 -92.42 REMARK 500 ASN B 360 18.13 58.85 REMARK 500 ALA B 387 -46.10 -132.25 REMARK 500 MET B 423 -2.76 84.27 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 A1389 DISTANCE = 6.04 ANGSTROMS REMARK 525 HOH A1390 DISTANCE = 6.10 ANGSTROMS REMARK 525 HOH A1391 DISTANCE = 7.05 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PLR A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FLC A 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide PLR B 1001 and LYS B REMARK 800 284 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4ZDO RELATED DB: PDB REMARK 900 RELATED ID: 4ZDP RELATED DB: PDB DBREF 4ZDL A 1 501 UNP Q9HD40 SPCS_HUMAN 1 501 DBREF 4ZDL B 1 501 UNP Q9HD40 SPCS_HUMAN 1 501 SEQADV 4ZDL SER A 325 UNP Q9HD40 THR 325 ENGINEERED MUTATION SEQADV 4ZDL SER B 325 UNP Q9HD40 THR 325 ENGINEERED MUTATION SEQRES 1 A 501 MET ASN ARG GLU SER PHE ALA ALA GLY GLU ARG LEU VAL SEQRES 2 A 501 SER PRO ALA TYR VAL ARG GLN GLY CYS GLU ALA ARG ARG SEQRES 3 A 501 SER HIS GLU HIS LEU ILE ARG LEU LEU LEU GLU LYS GLY SEQRES 4 A 501 LYS CYS PRO GLU ASN GLY TRP ASP GLU SER THR LEU GLU SEQRES 5 A 501 LEU PHE LEU HIS GLU LEU ALA ILE MET ASP SER ASN ASN SEQRES 6 A 501 PHE LEU GLY ASN CYS GLY VAL GLY GLU ARG GLU GLY ARG SEQRES 7 A 501 VAL ALA SER ALA LEU VAL ALA ARG ARG HIS TYR ARG PHE SEQRES 8 A 501 ILE HIS GLY ILE GLY ARG SER GLY ASP ILE SER ALA VAL SEQRES 9 A 501 GLN PRO LYS ALA ALA GLY SER SER LEU LEU ASN LYS ILE SEQRES 10 A 501 THR ASN SER LEU VAL LEU ASP ILE ILE LYS LEU ALA GLY SEQRES 11 A 501 VAL HIS THR VAL ALA ASN CYS PHE VAL VAL PRO MET ALA SEQRES 12 A 501 THR GLY MET SER LEU THR LEU CYS PHE LEU THR LEU ARG SEQRES 13 A 501 HIS LYS ARG PRO LYS ALA LYS TYR ILE ILE TRP PRO ARG SEQRES 14 A 501 ILE ASP GLN LYS SER CYS PHE LYS SER MET ILE THR ALA SEQRES 15 A 501 GLY PHE GLU PRO VAL VAL ILE GLU ASN VAL LEU GLU GLY SEQRES 16 A 501 ASP GLU LEU ARG THR ASP LEU LYS ALA VAL GLU ALA LYS SEQRES 17 A 501 VAL GLN GLU LEU GLY PRO ASP CYS ILE LEU CYS ILE HIS SEQRES 18 A 501 SER THR THR SER CYS PHE ALA PRO ARG VAL PRO ASP ARG SEQRES 19 A 501 LEU GLU GLU LEU ALA VAL ILE CYS ALA ASN TYR ASP ILE SEQRES 20 A 501 PRO HIS ILE VAL ASN ASN ALA TYR GLY VAL GLN SER SER SEQRES 21 A 501 LYS CYS MET HIS LEU ILE GLN GLN GLY ALA ARG VAL GLY SEQRES 22 A 501 ARG ILE ASP ALA PHE VAL GLN SER LEU ASP LYS ASN PHE SEQRES 23 A 501 MET VAL PRO VAL GLY GLY ALA ILE ILE ALA GLY PHE ASN SEQRES 24 A 501 ASP SER PHE ILE GLN GLU ILE SER LYS MET TYR PRO GLY SEQRES 25 A 501 ARG ALA SER ALA SER PRO SER LEU ASP VAL LEU ILE SER SEQRES 26 A 501 LEU LEU SER LEU GLY SER ASN GLY TYR LYS LYS LEU LEU SEQRES 27 A 501 LYS GLU ARG LYS GLU MET PHE SER TYR LEU SER ASN GLN SEQRES 28 A 501 ILE LYS LYS LEU SER GLU ALA TYR ASN GLU ARG LEU LEU SEQRES 29 A 501 HIS THR PRO HIS ASN PRO ILE SER LEU ALA MET THR LEU SEQRES 30 A 501 LYS THR LEU ASP GLU HIS ARG ASP LYS ALA VAL THR GLN SEQRES 31 A 501 LEU GLY SER MET LEU PHE THR ARG GLN VAL SER GLY ALA SEQRES 32 A 501 ARG VAL VAL PRO LEU GLY SER MET GLN THR VAL SER GLY SEQRES 33 A 501 TYR THR PHE ARG GLY PHE MET SER HIS THR ASN ASN TYR SEQRES 34 A 501 PRO CYS ALA TYR LEU ASN ALA ALA SER ALA ILE GLY MET SEQRES 35 A 501 LYS MET GLN ASP VAL ASP LEU PHE ILE LYS ARG LEU ASP SEQRES 36 A 501 ARG CYS LEU LYS ALA VAL ARG LYS GLU ARG SER LYS GLU SEQRES 37 A 501 SER ASP ASP ASN TYR ASP LYS THR GLU ASP VAL ASP ILE SEQRES 38 A 501 GLU GLU MET ALA LEU LYS LEU ASP ASN VAL LEU LEU ASP SEQRES 39 A 501 THR TYR GLN ASP ALA SER SER SEQRES 1 B 501 MET ASN ARG GLU SER PHE ALA ALA GLY GLU ARG LEU VAL SEQRES 2 B 501 SER PRO ALA TYR VAL ARG GLN GLY CYS GLU ALA ARG ARG SEQRES 3 B 501 SER HIS GLU HIS LEU ILE ARG LEU LEU LEU GLU LYS GLY SEQRES 4 B 501 LYS CYS PRO GLU ASN GLY TRP ASP GLU SER THR LEU GLU SEQRES 5 B 501 LEU PHE LEU HIS GLU LEU ALA ILE MET ASP SER ASN ASN SEQRES 6 B 501 PHE LEU GLY ASN CYS GLY VAL GLY GLU ARG GLU GLY ARG SEQRES 7 B 501 VAL ALA SER ALA LEU VAL ALA ARG ARG HIS TYR ARG PHE SEQRES 8 B 501 ILE HIS GLY ILE GLY ARG SER GLY ASP ILE SER ALA VAL SEQRES 9 B 501 GLN PRO LYS ALA ALA GLY SER SER LEU LEU ASN LYS ILE SEQRES 10 B 501 THR ASN SER LEU VAL LEU ASP ILE ILE LYS LEU ALA GLY SEQRES 11 B 501 VAL HIS THR VAL ALA ASN CYS PHE VAL VAL PRO MET ALA SEQRES 12 B 501 THR GLY MET SER LEU THR LEU CYS PHE LEU THR LEU ARG SEQRES 13 B 501 HIS LYS ARG PRO LYS ALA LYS TYR ILE ILE TRP PRO ARG SEQRES 14 B 501 ILE ASP GLN LYS SER CYS PHE LYS SER MET ILE THR ALA SEQRES 15 B 501 GLY PHE GLU PRO VAL VAL ILE GLU ASN VAL LEU GLU GLY SEQRES 16 B 501 ASP GLU LEU ARG THR ASP LEU LYS ALA VAL GLU ALA LYS SEQRES 17 B 501 VAL GLN GLU LEU GLY PRO ASP CYS ILE LEU CYS ILE HIS SEQRES 18 B 501 SER THR THR SER CYS PHE ALA PRO ARG VAL PRO ASP ARG SEQRES 19 B 501 LEU GLU GLU LEU ALA VAL ILE CYS ALA ASN TYR ASP ILE SEQRES 20 B 501 PRO HIS ILE VAL ASN ASN ALA TYR GLY VAL GLN SER SER SEQRES 21 B 501 LYS CYS MET HIS LEU ILE GLN GLN GLY ALA ARG VAL GLY SEQRES 22 B 501 ARG ILE ASP ALA PHE VAL GLN SER LEU ASP LYS ASN PHE SEQRES 23 B 501 MET VAL PRO VAL GLY GLY ALA ILE ILE ALA GLY PHE ASN SEQRES 24 B 501 ASP SER PHE ILE GLN GLU ILE SER LYS MET TYR PRO GLY SEQRES 25 B 501 ARG ALA SER ALA SER PRO SER LEU ASP VAL LEU ILE SER SEQRES 26 B 501 LEU LEU SER LEU GLY SER ASN GLY TYR LYS LYS LEU LEU SEQRES 27 B 501 LYS GLU ARG LYS GLU MET PHE SER TYR LEU SER ASN GLN SEQRES 28 B 501 ILE LYS LYS LEU SER GLU ALA TYR ASN GLU ARG LEU LEU SEQRES 29 B 501 HIS THR PRO HIS ASN PRO ILE SER LEU ALA MET THR LEU SEQRES 30 B 501 LYS THR LEU ASP GLU HIS ARG ASP LYS ALA VAL THR GLN SEQRES 31 B 501 LEU GLY SER MET LEU PHE THR ARG GLN VAL SER GLY ALA SEQRES 32 B 501 ARG VAL VAL PRO LEU GLY SER MET GLN THR VAL SER GLY SEQRES 33 B 501 TYR THR PHE ARG GLY PHE MET SER HIS THR ASN ASN TYR SEQRES 34 B 501 PRO CYS ALA TYR LEU ASN ALA ALA SER ALA ILE GLY MET SEQRES 35 B 501 LYS MET GLN ASP VAL ASP LEU PHE ILE LYS ARG LEU ASP SEQRES 36 B 501 ARG CYS LEU LYS ALA VAL ARG LYS GLU ARG SER LYS GLU SEQRES 37 B 501 SER ASP ASP ASN TYR ASP LYS THR GLU ASP VAL ASP ILE SEQRES 38 B 501 GLU GLU MET ALA LEU LYS LEU ASP ASN VAL LEU LEU ASP SEQRES 39 B 501 THR TYR GLN ASP ALA SER SER HET PLR A1001 15 HET FLC A1002 18 HET PLR B1001 15 HETNAM PLR (5-HYDROXY-4,6-DIMETHYLPYRIDIN-3-YL)METHYL DIHYDROGEN HETNAM 2 PLR PHOSPHATE HETNAM FLC CITRATE ANION HETSYN PLR 4'-DEOXYPYRIDOXINE PHOSPHATE FORMUL 3 PLR 2(C8 H12 N O5 P) FORMUL 4 FLC C6 H5 O7 3- FORMUL 6 HOH *530(H2 O) HELIX 1 AA1 GLY A 21 GLY A 39 1 19 HELIX 2 AA2 ASP A 47 ILE A 60 1 14 HELIX 3 AA3 MET A 61 PHE A 66 5 6 HELIX 4 AA4 SER A 81 HIS A 88 1 8 HELIX 5 AA5 ALA A 108 ALA A 129 1 22 HELIX 6 AA6 ALA A 143 ARG A 159 1 17 HELIX 7 AA7 GLN A 172 ALA A 182 1 11 HELIX 8 AA8 ASP A 201 GLY A 213 1 13 HELIX 9 AA9 ARG A 234 TYR A 245 1 12 HELIX 10 AB1 SER A 259 GLY A 273 1 15 HELIX 11 AB2 LEU A 282 MET A 287 1 6 HELIX 12 AB3 ASN A 299 MET A 309 1 11 HELIX 13 AB4 ALA A 316 ALA A 358 1 43 HELIX 14 AB5 ALA A 387 ARG A 398 1 12 HELIX 15 AB6 LYS A 443 ARG A 462 1 20 HELIX 16 AB7 GLY B 21 GLY B 39 1 19 HELIX 17 AB8 ASP B 47 ILE B 60 1 14 HELIX 18 AB9 MET B 61 PHE B 66 5 6 HELIX 19 AC1 SER B 81 HIS B 88 1 8 HELIX 20 AC2 ALA B 108 ALA B 129 1 22 HELIX 21 AC3 ALA B 143 ARG B 159 1 17 HELIX 22 AC4 GLN B 172 ALA B 182 1 11 HELIX 23 AC5 ASP B 201 GLY B 213 1 13 HELIX 24 AC6 ARG B 234 TYR B 245 1 12 HELIX 25 AC7 SER B 259 GLY B 273 1 15 HELIX 26 AC8 LEU B 282 MET B 287 1 6 HELIX 27 AC9 ASN B 299 TYR B 310 1 12 HELIX 28 AD1 ALA B 316 ALA B 358 1 43 HELIX 29 AD2 ALA B 387 ARG B 398 1 12 HELIX 30 AD3 LYS B 443 ALA B 460 1 18 SHEET 1 AA1 7 ASN A 136 VAL A 140 0 SHEET 2 AA1 7 ALA A 293 GLY A 297 -1 O ALA A 293 N VAL A 140 SHEET 3 AA1 7 ALA A 277 SER A 281 -1 N PHE A 278 O ALA A 296 SHEET 4 AA1 7 HIS A 249 ASN A 252 1 N VAL A 251 O ALA A 277 SHEET 5 AA1 7 ILE A 217 THR A 223 1 N SER A 222 O ASN A 252 SHEET 6 AA1 7 TYR A 164 PRO A 168 1 N TYR A 164 O LEU A 218 SHEET 7 AA1 7 GLU A 185 ILE A 189 1 O VAL A 187 N ILE A 165 SHEET 1 AA2 2 ASN A 191 GLU A 194 0 SHEET 2 AA2 2 GLU A 197 THR A 200 -1 O ARG A 199 N VAL A 192 SHEET 1 AA3 3 SER A 372 THR A 376 0 SHEET 2 AA3 3 TYR A 433 ALA A 437 -1 O ALA A 436 N LEU A 373 SHEET 3 AA3 3 ARG A 404 VAL A 406 -1 N ARG A 404 O ASN A 435 SHEET 1 AA4 2 MET A 411 VAL A 414 0 SHEET 2 AA4 2 TYR A 417 ARG A 420 -1 O TYR A 417 N VAL A 414 SHEET 1 AA5 7 ASN B 136 VAL B 140 0 SHEET 2 AA5 7 ALA B 293 GLY B 297 -1 O ALA B 293 N VAL B 140 SHEET 3 AA5 7 ALA B 277 SER B 281 -1 N PHE B 278 O ALA B 296 SHEET 4 AA5 7 HIS B 249 ASN B 252 1 N VAL B 251 O ALA B 277 SHEET 5 AA5 7 ILE B 217 THR B 223 1 N SER B 222 O ASN B 252 SHEET 6 AA5 7 TYR B 164 PRO B 168 1 N TYR B 164 O LEU B 218 SHEET 7 AA5 7 GLU B 185 ILE B 189 1 O VAL B 187 N ILE B 165 SHEET 1 AA6 2 VAL B 192 GLU B 194 0 SHEET 2 AA6 2 GLU B 197 ARG B 199 -1 O GLU B 197 N GLU B 194 SHEET 1 AA7 3 SER B 372 THR B 376 0 SHEET 2 AA7 3 TYR B 433 ALA B 437 -1 O ALA B 436 N LEU B 373 SHEET 3 AA7 3 VAL B 405 VAL B 406 -1 N VAL B 406 O TYR B 433 SHEET 1 AA8 2 GLN B 412 VAL B 414 0 SHEET 2 AA8 2 TYR B 417 PHE B 419 -1 O PHE B 419 N GLN B 412 LINK NZ LYS A 284 C4A PLR A1001 1555 1555 1.35 LINK NZ LYS B 284 C4A PLR B1001 1555 1555 1.35 CISPEP 1 ALA A 228 PRO A 229 0 6.75 CISPEP 2 ALA B 228 PRO B 229 0 7.38 SITE 1 AC1 19 ARG A 75 SER A 98 ALA A 143 THR A 144 SITE 2 AC1 19 GLY A 145 ILE A 170 GLN A 172 SER A 174 SITE 3 AC1 19 ASN A 252 ALA A 254 TYR A 255 LYS A 284 SITE 4 AC1 19 GLY A 312 ARG A 313 FLC A1002 HOH A1110 SITE 5 AC1 19 HOH A1184 HOH A1219 HOH A1245 SITE 1 AC2 11 ARG A 75 ARG A 97 SER A 98 GLN A 105 SITE 2 AC2 11 LYS A 107 ARG A 313 ARG A 404 PLR A1001 SITE 3 AC2 11 HOH A1112 HOH A1154 HOH A1174 SITE 1 AC3 22 GLU B 74 ARG B 75 ALA B 143 THR B 144 SITE 2 AC3 22 GLY B 145 ILE B 170 GLN B 172 SER B 174 SITE 3 AC3 22 ASN B 252 ALA B 254 TYR B 255 SER B 281 SITE 4 AC3 22 LEU B 282 ASP B 283 ASN B 285 PHE B 286 SITE 5 AC3 22 GLY B 312 ARG B 313 ILE B 440 HOH B1110 SITE 6 AC3 22 HOH B1121 HOH B1126 CRYST1 68.016 83.151 193.140 90.00 90.00 90.00 P 21 21 2 8 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 0.014702 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012026 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005178 0.00000