HEADER TRANSFERASE 03-MAY-17 5NV8 TITLE STRUCTURAL BASIS FOR EARP-MEDIATED ARGININE GLYCOSYLATION OF TITLE 2 TRANSLATION ELONGATION FACTOR EF-P COMPND MOL_ID: 1; COMPND 2 MOLECULE: EF-P ARGININE 32 RHAMNOSYL-TRANSFERASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS PUTIDA KT2440; SOURCE 3 ORGANISM_TAXID: 160488; SOURCE 4 STRAIN: ATCC 47054 / DSM 6125 / NCIMB 11950 / KT2440; SOURCE 5 GENE: EARP, PP_1857; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS GLYCOSYLTRANSFERASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR J.MACOSEK,R.KRAFCZYK,P.K.A.JAGTAP,J.LASSAKA,J.HENNIG REVDAT 3 18-OCT-17 5NV8 1 AUTHOR REVDAT 2 11-OCT-17 5NV8 1 JRNL REVDAT 1 04-OCT-17 5NV8 0 JRNL AUTH R.KRAFCZYK,J.MACOSEK,P.K.A.JAGTAP,D.GAST,S.WUNDER,P.MITRA, JRNL AUTH 2 A.K.JHA,J.ROHR,A.HOFFMANN-RODER,K.JUNG,J.HENNIG,J.LASSAK JRNL TITL STRUCTURAL BASIS FOR EARP-MEDIATED ARGININE GLYCOSYLATION OF JRNL TITL 2 TRANSLATION ELONGATION FACTOR EF-P. JRNL REF MBIO V. 8 2017 JRNL REFN ESSN 2150-7511 JRNL PMID 28951478 JRNL DOI 10.1128/MBIO.01412-17 REMARK 2 REMARK 2 RESOLUTION. 2.29 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.11.1_2575: ???) 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) : 2.29 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.56 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 3 NUMBER OF REFLECTIONS : 17538 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.292 REMARK 3 R VALUE (WORKING SET) : 0.289 REMARK 3 FREE R VALUE : 0.339 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 877 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 46.5655 - 4.1680 0.93 2718 144 0.2773 0.3008 REMARK 3 2 4.1680 - 3.3086 0.97 2751 144 0.2624 0.3531 REMARK 3 3 3.3086 - 2.8904 0.98 2809 148 0.2918 0.3302 REMARK 3 4 2.8904 - 2.6262 0.98 2799 148 0.3028 0.3682 REMARK 3 5 2.6262 - 2.4379 0.98 2750 144 0.3312 0.3882 REMARK 3 6 2.4379 - 2.2942 0.99 2834 149 0.3447 0.3777 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) : 0.430 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 38.920 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 : 0.003 2394 REMARK 3 ANGLE : 0.664 3262 REMARK 3 CHIRALITY : 0.041 362 REMARK 3 PLANARITY : 0.005 417 REMARK 3 DIHEDRAL : 6.206 1886 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 2 THROUGH 30 ) REMARK 3 ORIGIN FOR THE GROUP (A): 62.3148 26.9584 10.1810 REMARK 3 T TENSOR REMARK 3 T11: 0.4889 T22: 0.4132 REMARK 3 T33: 0.4287 T12: 0.0674 REMARK 3 T13: -0.0947 T23: -0.4905 REMARK 3 L TENSOR REMARK 3 L11: 0.3564 L22: 2.8365 REMARK 3 L33: 2.8115 L12: 1.0370 REMARK 3 L13: 0.3019 L23: 0.8917 REMARK 3 S TENSOR REMARK 3 S11: -0.0424 S12: 0.9064 S13: -0.8315 REMARK 3 S21: -0.8421 S22: -0.9132 S23: 0.6270 REMARK 3 S31: 0.1459 S32: -0.5503 S33: -0.8084 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 31 THROUGH 128 ) REMARK 3 ORIGIN FOR THE GROUP (A): 65.8685 20.1030 7.4661 REMARK 3 T TENSOR REMARK 3 T11: 0.3399 T22: 0.3310 REMARK 3 T33: 0.5188 T12: 0.0936 REMARK 3 T13: -0.0855 T23: -0.0992 REMARK 3 L TENSOR REMARK 3 L11: 0.6110 L22: 3.1391 REMARK 3 L33: 1.7871 L12: -0.2488 REMARK 3 L13: 0.6727 L23: 1.1763 REMARK 3 S TENSOR REMARK 3 S11: 0.4507 S12: 0.5497 S13: -0.7167 REMARK 3 S21: -0.3494 S22: -0.1803 S23: -0.1228 REMARK 3 S31: 0.2298 S32: 0.0704 S33: -0.1127 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 132 THROUGH 377 ) REMARK 3 ORIGIN FOR THE GROUP (A): 49.3151 40.4994 21.3155 REMARK 3 T TENSOR REMARK 3 T11: 0.2782 T22: 0.2236 REMARK 3 T33: 0.3801 T12: -0.0150 REMARK 3 T13: -0.0332 T23: -0.0496 REMARK 3 L TENSOR REMARK 3 L11: 4.0326 L22: 2.7193 REMARK 3 L33: 0.5770 L12: -2.6320 REMARK 3 L13: -1.1010 L23: 0.3139 REMARK 3 S TENSOR REMARK 3 S11: -0.0138 S12: 0.2810 S13: -0.3042 REMARK 3 S21: -0.0203 S22: -0.1666 S23: 0.4318 REMARK 3 S31: 0.1742 S32: -0.0883 S33: 0.0934 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 5NV8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 04-MAY-17. REMARK 100 THE DEPOSITION ID IS D_1200004771. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-SEP-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.87290 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17539 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.298 REMARK 200 RESOLUTION RANGE LOW (A) : 46.542 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.13000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.7300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.36 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.5 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : 0.59000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.870 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: CRANK2 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.48 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M AMMONIUM ACETATE, 0.1M BIS-TRIS REMARK 280 AND 27% (W/V) PEG 3350, PH 6, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 4 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 -Y,X,Z REMARK 290 4555 Y,-X,Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -Y+1/2,X+1/2,Z+1/2 REMARK 290 8555 Y+1/2,-X+1/2,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 -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 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 65.84000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 65.84000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 23.12000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 65.84000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 65.84000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 23.12000 REMARK 290 SMTRY1 7 0.000000 -1.000000 0.000000 65.84000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 65.84000 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 23.12000 REMARK 290 SMTRY1 8 0.000000 1.000000 0.000000 65.84000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 65.84000 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 23.12000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1000 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15260 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.0 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 MET A -12 REMARK 465 GLY A -11 REMARK 465 SER A -10 REMARK 465 SER A -9 REMARK 465 HIS A -8 REMARK 465 HIS A -7 REMARK 465 HIS A -6 REMARK 465 HIS A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 SER A -2 REMARK 465 GLN A -1 REMARK 465 ASP A 0 REMARK 465 PRO A 1 REMARK 465 VAL A 12 REMARK 465 ASN A 44 REMARK 465 ALA A 45 REMARK 465 PHE A 46 REMARK 465 THR A 47 REMARK 465 PRO A 48 REMARK 465 MET A 49 REMARK 465 CYS A 50 REMARK 465 PRO A 51 REMARK 465 GLY A 52 REMARK 465 GLN A 59 REMARK 465 GLN A 60 REMARK 465 TRP A 61 REMARK 465 GLN A 62 REMARK 465 HIS A 63 REMARK 465 GLY A 64 REMARK 465 VAL A 65 REMARK 465 ASP A 66 REMARK 465 VAL A 67 REMARK 465 ARG A 68 REMARK 465 HIS A 69 REMARK 465 TRP A 70 REMARK 465 PRO A 71 REMARK 465 ALA A 72 REMARK 465 PRO A 76 REMARK 465 VAL A 77 REMARK 465 ALA A 78 REMARK 465 PRO A 79 REMARK 465 ALA A 80 REMARK 465 ASP A 81 REMARK 465 VAL A 82 REMARK 465 VAL A 83 REMARK 465 ILE A 84 REMARK 465 ALA A 88 REMARK 465 ARG A 100 REMARK 465 ALA A 101 REMARK 465 ARG A 102 REMARK 465 PRO A 103 REMARK 465 GLN A 104 REMARK 465 PRO A 105 REMARK 465 PRO A 106 REMARK 465 LEU A 107 REMARK 465 TRP A 108 REMARK 465 LEU A 109 REMARK 465 ASN A 110 REMARK 465 LEU A 111 REMARK 465 GLU A 112 REMARK 465 TYR A 113 REMARK 465 LEU A 114 REMARK 465 SER A 115 REMARK 465 ALA A 116 REMARK 465 GLU A 117 REMARK 465 ASP A 118 REMARK 465 TRP A 119 REMARK 465 VAL A 120 REMARK 465 GLU A 121 REMARK 465 GLY A 122 REMARK 465 CYS A 123 REMARK 465 HIS A 124 REMARK 465 GLY A 125 REMARK 465 LEU A 126 REMARK 465 PRO A 129 REMARK 465 GLN A 130 REMARK 465 PRO A 131 REMARK 465 THR A 147 REMARK 465 GLY A 148 REMARK 465 GLN A 293 REMARK 465 ASP A 294 REMARK 465 GLU A 295 REMARK 465 ASN A 296 REMARK 465 ALA A 297 REMARK 465 HIS A 298 REMARK 465 TRP A 299 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 ILE A 7 CG1 CG2 CD1 REMARK 470 PHE A 8 CG CD1 CD2 CE1 CE2 CZ REMARK 470 TRP A 39 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP A 39 CZ3 CH2 REMARK 470 ASP A 42 CG OD1 OD2 REMARK 470 TRP A 74 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP A 74 CZ3 CH2 REMARK 470 PHE A 87 CD1 CD2 CE1 CE2 CZ REMARK 470 CYS A 89 SG REMARK 470 GLN A 90 CG CD OE1 NE2 REMARK 470 TYR A 95 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 GLU A 97 CD OE1 OE2 REMARK 470 ARG A 135 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 136 CE NZ REMARK 470 PHE A 138 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS A 146 CG CD CE NZ REMARK 470 ARG A 171 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 218 CG CD OE1 NE2 REMARK 470 TYR A 291 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 VAL A 292 CG1 CG2 REMARK 470 GLU A 300 CG CD OE1 OE2 REMARK 470 LYS A 301 CE NZ REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 PHE A 138 CA CB 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 O HOH A 572 O HOH A 588 1.76 REMARK 500 O HOH A 687 O HOH A 693 1.84 REMARK 500 O HOH A 686 O HOH A 695 1.84 REMARK 500 O PHE A 143 O HOH A 501 1.90 REMARK 500 O HOH A 667 O HOH A 679 1.93 REMARK 500 O MET A 99 O HOH A 502 1.98 REMARK 500 O HOH A 623 O HOH A 624 1.98 REMARK 500 O HOH A 620 O HOH A 686 2.02 REMARK 500 O VAL A 270 O HOH A 503 2.03 REMARK 500 O HOH A 674 O HOH A 685 2.03 REMARK 500 O PRO A 127 O HOH A 504 2.05 REMARK 500 NH2 ARG A 310 O HOH A 505 2.06 REMARK 500 O HOH A 507 O HOH A 609 2.07 REMARK 500 N31 TRH A 401 O HOH A 506 2.08 REMARK 500 O HOH A 642 O HOH A 650 2.09 REMARK 500 OD2 ASP A 41 O HOH A 507 2.10 REMARK 500 O HOH A 504 O HOH A 631 2.11 REMARK 500 NH2 ARG A 170 O HOH A 508 2.11 REMARK 500 O GLN A 359 O HOH A 509 2.11 REMARK 500 O HOH A 554 O HOH A 570 2.12 REMARK 500 OE2 GLU A 231 O HOH A 510 2.12 REMARK 500 O HOH A 640 O HOH A 683 2.12 REMARK 500 O HOH A 552 O HOH A 623 2.13 REMARK 500 O HOH A 517 O HOH A 628 2.14 REMARK 500 O HOH A 698 O HOH A 705 2.14 REMARK 500 O HOH A 607 O HOH A 627 2.14 REMARK 500 OD2 ASP A 54 O HOH A 511 2.15 REMARK 500 N TRP A 74 O HOH A 512 2.16 REMARK 500 O HOH A 507 O HOH A 620 2.18 REMARK 500 O THR A 56 O HOH A 513 2.19 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 HOH A 686 O HOH A 688 1554 2.19 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 10 -124.97 -115.68 REMARK 500 ASN A 14 -105.23 -147.16 REMARK 500 ASP A 54 -108.69 -147.99 REMARK 500 PRO A 92 41.68 -101.95 REMARK 500 TYR A 95 86.33 -68.61 REMARK 500 GLU A 97 15.23 -66.39 REMARK 500 PHE A 138 -86.12 -88.49 REMARK 500 PHE A 138 -86.22 -88.41 REMARK 500 ASP A 145 47.67 -73.06 REMARK 500 TYR A 193 -158.60 -89.60 REMARK 500 ARG A 220 7.13 -68.42 REMARK 500 GLU A 231 -159.92 -95.14 REMARK 500 VAL A 253 -145.66 -85.52 REMARK 500 TYR A 291 60.19 21.71 REMARK 500 SER A 376 -88.12 57.11 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 693 DISTANCE = 5.98 ANGSTROMS REMARK 525 HOH A 694 DISTANCE = 6.16 ANGSTROMS REMARK 525 HOH A 695 DISTANCE = 6.26 ANGSTROMS REMARK 525 HOH A 696 DISTANCE = 6.62 ANGSTROMS REMARK 525 HOH A 697 DISTANCE = 6.77 ANGSTROMS REMARK 525 HOH A 698 DISTANCE = 6.78 ANGSTROMS REMARK 525 HOH A 699 DISTANCE = 6.79 ANGSTROMS REMARK 525 HOH A 700 DISTANCE = 6.97 ANGSTROMS REMARK 525 HOH A 701 DISTANCE = 7.22 ANGSTROMS REMARK 525 HOH A 702 DISTANCE = 7.83 ANGSTROMS REMARK 525 HOH A 703 DISTANCE = 7.87 ANGSTROMS REMARK 525 HOH A 704 DISTANCE = 8.25 ANGSTROMS REMARK 525 HOH A 705 DISTANCE = 8.25 ANGSTROMS REMARK 525 HOH A 706 DISTANCE = 8.30 ANGSTROMS REMARK 525 HOH A 707 DISTANCE = 8.36 ANGSTROMS REMARK 525 HOH A 708 DISTANCE = 8.89 ANGSTROMS REMARK 525 HOH A 709 DISTANCE = 9.05 ANGSTROMS REMARK 525 HOH A 710 DISTANCE = 9.42 ANGSTROMS REMARK 615 REMARK 615 ZERO OCCUPANCY ATOM REMARK 615 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 615 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 615 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 615 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 615 M RES C SSEQI REMARK 615 TRH A 401 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue TRH A 401 DBREF 5NV8 A 2 377 UNP Q88LS1 Q88LS1_PSEPK 2 377 SEQADV 5NV8 MET A -12 UNP Q88LS1 INITIATING METHIONINE SEQADV 5NV8 GLY A -11 UNP Q88LS1 EXPRESSION TAG SEQADV 5NV8 SER A -10 UNP Q88LS1 EXPRESSION TAG SEQADV 5NV8 SER A -9 UNP Q88LS1 EXPRESSION TAG SEQADV 5NV8 HIS A -8 UNP Q88LS1 EXPRESSION TAG SEQADV 5NV8 HIS A -7 UNP Q88LS1 EXPRESSION TAG SEQADV 5NV8 HIS A -6 UNP Q88LS1 EXPRESSION TAG SEQADV 5NV8 HIS A -5 UNP Q88LS1 EXPRESSION TAG SEQADV 5NV8 HIS A -4 UNP Q88LS1 EXPRESSION TAG SEQADV 5NV8 HIS A -3 UNP Q88LS1 EXPRESSION TAG SEQADV 5NV8 SER A -2 UNP Q88LS1 EXPRESSION TAG SEQADV 5NV8 GLN A -1 UNP Q88LS1 EXPRESSION TAG SEQADV 5NV8 ASP A 0 UNP Q88LS1 EXPRESSION TAG SEQADV 5NV8 PRO A 1 UNP Q88LS1 EXPRESSION TAG SEQRES 1 A 390 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER GLN ASP SEQRES 2 A 390 PRO LYS ALA THR TRP ASP ILE PHE CYS SER VAL VAL ASP SEQRES 3 A 390 ASN TYR GLY ASP ILE GLY VAL THR TRP ARG LEU ALA ARG SEQRES 4 A 390 GLN LEU VAL ALA GLU HIS GLY LEU ALA VAL ARG LEU TRP SEQRES 5 A 390 VAL ASP ASP LEU ASN ALA PHE THR PRO MET CYS PRO GLY SEQRES 6 A 390 ALA ASP ALA THR ALA ALA GLN GLN TRP GLN HIS GLY VAL SEQRES 7 A 390 ASP VAL ARG HIS TRP PRO ALA ALA TRP LEU PRO VAL ALA SEQRES 8 A 390 PRO ALA ASP VAL VAL ILE GLY ALA PHE ALA CYS GLN LEU SEQRES 9 A 390 PRO ALA ALA TYR VAL GLU ALA MET ARG ALA ARG PRO GLN SEQRES 10 A 390 PRO PRO LEU TRP LEU ASN LEU GLU TYR LEU SER ALA GLU SEQRES 11 A 390 ASP TRP VAL GLU GLY CYS HIS GLY LEU PRO SER PRO GLN SEQRES 12 A 390 PRO ASN GLY LEU ARG LYS VAL PHE PHE PHE PRO GLY PHE SEQRES 13 A 390 THR ASP LYS THR GLY GLY LEU LEU ARG GLU GLY SER LEU SEQRES 14 A 390 LEU ALA ARG ARG ASP GLY PHE GLN GLN SER ALA GLU ALA SEQRES 15 A 390 ARG ARG ALA PHE LEU GLN GLY LEU GLY VAL ASP LEU VAL SEQRES 16 A 390 PRO GLY ALA LEU LEU ILE SER LEU PHE ALA TYR GLU ASN SEQRES 17 A 390 PRO GLN LEU GLY ASN TRP LEU ASP ALA LEU ALA THR ALA SEQRES 18 A 390 ASP GLN PRO CYS HIS LEU LEU VAL PRO GLN GLY ARG VAL SEQRES 19 A 390 VAL ALA GLY LEU SER GLN TRP LEU GLY GLU GLY PRO LEU SEQRES 20 A 390 HIS VAL GLY ASP VAL ARG THR ARG GLY ALA LEU THR VAL SEQRES 21 A 390 GLN VAL LEU PRO PHE VAL SER GLN ASP ASP PHE ASP ARG SEQRES 22 A 390 LEU LEU TRP SER CYS ASP PHE ASN ALA VAL ARG GLY GLU SEQRES 23 A 390 ASP SER PHE VAL ARG ALA GLN TRP ALA GLY GLN PRO MET SEQRES 24 A 390 LEU TRP HIS ILE TYR VAL GLN ASP GLU ASN ALA HIS TRP SEQRES 25 A 390 GLU LYS LEU GLU ALA PHE LEU ALA HIS TYR ARG CYS GLY SEQRES 26 A 390 LEU SER ASP ASP ALA ASP ALA ALA LEU LEU GLY LEU TRP SEQRES 27 A 390 ARG ALA TRP ASN MET ASP PHE ASP MET GLY GLN ALA TRP SEQRES 28 A 390 ARG ALA ALA ARG GLN HIS TRP PRO GLU LEU GLN GLN HIS SEQRES 29 A 390 ALA ARG LEU TRP GLY ALA ARG GLN ALA ALA GLN PRO ASP SEQRES 30 A 390 LEU ALA THR ALA LEU VAL HIS PHE TYR ARG ASN SER LEU HET TRH A 401 35 HETNAM TRH 2'-DEOXY-THYMIDINE-BETA-L-RHAMNOSE FORMUL 2 TRH C16 H26 N2 O15 P2 FORMUL 3 HOH *210(H2 O) HELIX 1 AA1 GLY A 16 GLU A 31 1 16 HELIX 2 AA2 SER A 155 GLN A 165 1 11 HELIX 3 AA3 SER A 166 LEU A 177 1 12 HELIX 4 AA4 GLN A 197 ALA A 208 1 12 HELIX 5 AA5 VAL A 221 GLY A 230 1 10 HELIX 6 AA6 SER A 254 CYS A 265 1 12 HELIX 7 AA7 GLU A 273 GLY A 283 1 11 HELIX 8 AA8 LYS A 301 ARG A 310 1 10 HELIX 9 AA9 SER A 314 ASP A 331 1 18 HELIX 10 AB1 ASP A 333 GLN A 343 1 11 HELIX 11 AB2 HIS A 344 ALA A 361 1 18 HELIX 12 AB3 ASP A 364 ASN A 375 1 12 SHEET 1 AA1 2 THR A 4 ILE A 7 0 SHEET 2 AA1 2 ALA A 35 LEU A 38 1 O ALA A 35 N TRP A 5 SHEET 1 AA2 6 VAL A 239 ARG A 242 0 SHEET 2 AA2 6 LEU A 245 LEU A 250 -1 O VAL A 247 N ARG A 240 SHEET 3 AA2 6 CYS A 212 PRO A 217 1 N VAL A 216 O LEU A 250 SHEET 4 AA2 6 LEU A 186 LEU A 190 1 N LEU A 186 O HIS A 213 SHEET 5 AA2 6 PHE A 267 ARG A 271 1 O ALA A 269 N SER A 189 SHEET 6 AA2 6 MET A 286 HIS A 289 1 O LEU A 287 N VAL A 270 SITE 1 AC1 14 TYR A 15 GLY A 16 ASP A 17 PHE A 191 SITE 2 AC1 14 TYR A 193 PHE A 252 GLN A 255 PHE A 258 SITE 3 AC1 14 ARG A 271 GLY A 272 GLU A 273 ASP A 274 SITE 4 AC1 14 SER A 275 HOH A 506 CRYST1 131.680 131.680 46.240 90.00 90.00 90.00 I 4 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 0.007594 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007594 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021626 0.00000