PDB Short entry for 3H9V HEADER TRANSPORT PROTEIN 30-APR-09 3H9V TITLE CRYSTAL STRUCTURE OF THE ATP-GATED P2X4 ION CHANNEL IN THE CLOSED, APO TITLE 2 STATE AT 3.1 ANGSTROMS CAVEAT 3H9V NAG B 1 HAS WRONG CHIRALITY AT ATOM C1 NAG B 2 HAS WRONG CAVEAT 2 3H9V CHIRALITY AT ATOM C1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: P2X PURINOCEPTOR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 28-381; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DANIO RERIO; SOURCE 3 ORGANISM_COMMON: LEOPARD DANIO,ZEBRA DANIO,ZEBRA FISH; SOURCE 4 ORGANISM_TAXID: 7955; SOURCE 5 GENE: P2RX4A, P2X4.1; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: SF9; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: BACMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PFASTBAC KEYWDS P2X, PURINERGIC RECEPTOR, ION CHANNEL, CLOSED STATE, APO STATE, ION KEYWDS 2 TRANSPORT, IONIC CHANNEL, RECEPTOR, TRANSMEMBRANE, TRANSPORT, KEYWDS 3 TRANSPORT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR T.KAWATE,J.C.MICHEL,E.GOUAUX REVDAT 6 13-OCT-21 3H9V 1 SEQADV HETSYN REVDAT 5 29-JUL-20 3H9V 1 CAVEAT COMPND REMARK SEQADV REVDAT 5 2 1 HETNAM LINK SITE ATOM REVDAT 4 01-NOV-17 3H9V 1 REMARK REVDAT 3 13-JUL-11 3H9V 1 VERSN REVDAT 2 11-AUG-09 3H9V 1 JRNL REVDAT 1 28-JUL-09 3H9V 0 JRNL AUTH T.KAWATE,J.C.MICHEL,W.T.BIRDSONG,E.GOUAUX JRNL TITL CRYSTAL STRUCTURE OF THE ATP-GATED P2X(4) ION CHANNEL IN THE JRNL TITL 2 CLOSED STATE. JRNL REF NATURE V. 460 592 2009 JRNL REFN ISSN 0028-0836 JRNL PMID 19641588 JRNL DOI 10.1038/NATURE08198 REMARK 2 REMARK 2 RESOLUTION. 3.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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) : 3.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.11 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 90.7 REMARK 3 NUMBER OF REFLECTIONS : 14372 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.249 REMARK 3 R VALUE (WORKING SET) : 0.248 REMARK 3 FREE R VALUE : 0.278 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.070 REMARK 3 FREE R VALUE TEST SET COUNT : 729 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 29.1101 - 5.2929 0.89 2818 128 0.2596 0.2689 REMARK 3 2 5.2929 - 4.2052 0.93 2794 154 0.2013 0.2489 REMARK 3 3 4.2052 - 3.6748 0.94 2816 149 0.2362 0.2685 REMARK 3 4 3.6748 - 3.3393 0.94 2750 167 0.2590 0.3149 REMARK 3 5 3.3393 - 3.1000 0.84 2465 131 0.3281 0.3933 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 1.00 REMARK 3 K_SOL : 0.26 REMARK 3 B_SOL : 65.84 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.460 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 33.410 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 97.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 103.6 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -28.24000 REMARK 3 B22 (A**2) : -28.24000 REMARK 3 B33 (A**2) : 56.48000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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 2562 REMARK 3 ANGLE : 1.483 3499 REMARK 3 CHIRALITY : 0.091 410 REMARK 3 PLANARITY : 0.005 448 REMARK 3 DIHEDRAL : 21.766 1548 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 3H9V COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-JUN-09. REMARK 100 THE DEPOSITION ID IS D_1000052874. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-MAR-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-E REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14414 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.090 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 (%) : 90.1 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 18.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.09 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.20 REMARK 200 COMPLETENESS FOR SHELL (%) : 69.9 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : 0.48400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.800 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 76.51 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 5.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 2,000, 300MM MG(NO3)2, AND REMARK 280 100MM TRIS PH 8.4, AND 1MM GDCL3, VAPOR DIFFUSION, TEMPERATURE REMARK 280 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 2 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 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-Z REMARK 290 7555 X+2/3,Y+1/3,Z+1/3 REMARK 290 8555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 9555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 10555 Y+2/3,X+1/3,-Z+1/3 REMARK 290 11555 X-Y+2/3,-Y+1/3,-Z+1/3 REMARK 290 12555 -X+2/3,-X+Y+1/3,-Z+1/3 REMARK 290 13555 X+1/3,Y+2/3,Z+2/3 REMARK 290 14555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 15555 -X+Y+1/3,-X+2/3,Z+2/3 REMARK 290 16555 Y+1/3,X+2/3,-Z+2/3 REMARK 290 17555 X-Y+1/3,-Y+2/3,-Z+2/3 REMARK 290 18555 -X+1/3,-X+Y+2/3,-Z+2/3 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 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 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 0.00000 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 50.41800 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 29.10885 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 143.77200 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 50.41800 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 29.10885 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 143.77200 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 50.41800 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 29.10885 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 143.77200 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 50.41800 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 29.10885 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 143.77200 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 50.41800 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 29.10885 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 143.77200 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 50.41800 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 29.10885 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 143.77200 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 58.21769 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 287.54400 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 58.21769 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 287.54400 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 58.21769 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 287.54400 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 58.21769 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 287.54400 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 58.21769 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 287.54400 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 58.21769 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 287.54400 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 14010 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 45980 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -36.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 3 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 GD GD A 382 LIES ON A SPECIAL POSITION. REMARK 375 GD GD A 383 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 GLY A 26 REMARK 465 SER A 27 REMARK 465 SER A 28 REMARK 465 LYS A 29 REMARK 465 LYS A 30 REMARK 465 VAL A 31 REMARK 465 ARG A 137 REMARK 465 THR A 362 REMARK 465 PHE A 363 REMARK 465 MET A 364 REMARK 465 LYS A 365 REMARK 465 ARG A 366 REMARK 465 LYS A 367 REMARK 465 GLN A 368 REMARK 465 HIS A 369 REMARK 465 TYR A 370 REMARK 465 LYS A 371 REMARK 465 GLU A 372 REMARK 465 GLN A 373 REMARK 465 LYS A 374 REMARK 465 TYR A 375 REMARK 465 THR A 376 REMARK 465 TYR A 377 REMARK 465 VAL A 378 REMARK 465 ASP A 379 REMARK 465 ASP A 380 REMARK 465 PHE A 381 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 THR A 33 OG1 CG2 REMARK 470 LEU A 34 CG CD1 CD2 REMARK 470 ASN A 35 CG OD1 ND2 REMARK 470 ARG A 36 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 39 CG CD OE1 NE2 REMARK 470 ASN A 54 CG OD1 ND2 REMARK 470 ASP A 59 CG OD1 OD2 REMARK 470 THR A 60 OG1 CG2 REMARK 470 LYS A 70 CG CD CE NZ REMARK 470 GLU A 81 CG CD OE1 OE2 REMARK 470 ASP A 91 CG OD1 OD2 REMARK 470 LYS A 118 CG CD CE NZ REMARK 470 ARG A 133 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 136 CG CD CE NZ REMARK 470 PHE A 139 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ASN A 140 CG OD1 ND2 REMARK 470 ASP A 141 CG OD1 OD2 REMARK 470 ARG A 143 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 148 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 151 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 160 CG CD CE NZ REMARK 470 ARG A 187 CG CD NE CZ NH1 NH2 REMARK 470 ASN A 211 CG OD1 ND2 REMARK 470 LYS A 225 CG CD CE NZ REMARK 470 GLN A 270 CG CD OE1 NE2 REMARK 470 ARG A 276 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 304 CG CD CE NZ REMARK 470 GLN A 329 CG CD OE1 NE2 REMARK 470 ILE A 335 CG1 CG2 CD1 REMARK 470 ILE A 336 CG1 CG2 CD1 REMARK 470 LEU A 348 CG CD1 CD2 REMARK 470 VAL A 352 CG1 CG2 REMARK 470 VAL A 354 CG1 CG2 REMARK 470 ILE A 355 CG1 CG2 CD1 REMARK 470 TRP A 358 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP A 358 CZ3 CH2 REMARK 470 ILE A 359 CG1 CG2 CD1 REMARK 470 VAL A 360 CG1 CG2 REMARK 470 LEU A 361 CG CD1 CD2 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 O3 NAG B 1 O5 NAG B 2 2.13 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 46 -77.87 -66.19 REMARK 500 VAL A 89 -33.36 -39.23 REMARK 500 ALA A 90 -89.81 -43.72 REMARK 500 PRO A 96 -157.09 -103.87 REMARK 500 ASP A 99 -75.81 -59.64 REMARK 500 SER A 101 179.58 -51.48 REMARK 500 THR A 106 -33.07 -130.27 REMARK 500 ASN A 113 21.90 45.08 REMARK 500 SER A 166 -172.90 -177.88 REMARK 500 LEU A 182 53.90 -92.41 REMARK 500 ASN A 202 55.93 31.03 REMARK 500 LEU A 217 2.53 -69.98 REMARK 500 HIS A 219 8.80 -159.62 REMARK 500 ASP A 227 79.76 -115.60 REMARK 500 REMARK 500 REMARK: NULL DBREF 3H9V A 28 381 UNP Q6NYR1 Q6NYR1_DANRE 28 381 SEQADV 3H9V GLY A 26 UNP Q6NYR1 EXPRESSION TAG SEQADV 3H9V SER A 27 UNP Q6NYR1 EXPRESSION TAG SEQADV 3H9V PHE A 51 UNP Q6NYR1 CYS 51 ENGINEERED MUTATION SEQADV 3H9V LYS A 78 UNP Q6NYR1 ASN 78 ENGINEERED MUTATION SEQADV 3H9V ARG A 187 UNP Q6NYR1 ASN 187 ENGINEERED MUTATION SEQADV 3H9V ARG A 252 UNP Q6NYR1 HIS 252 ENGINEERED MUTATION SEQRES 1 A 356 GLY SER SER LYS LYS VAL GLY THR LEU ASN ARG PHE THR SEQRES 2 A 356 GLN ALA LEU VAL ILE ALA TYR VAL ILE GLY TYR VAL PHE SEQRES 3 A 356 VAL TYR ASN LYS GLY TYR GLN ASP THR ASP THR VAL LEU SEQRES 4 A 356 SER SER VAL THR THR LYS VAL LYS GLY ILE ALA LEU THR SEQRES 5 A 356 LYS THR SER GLU LEU GLY GLU ARG ILE TRP ASP VAL ALA SEQRES 6 A 356 ASP TYR ILE ILE PRO PRO GLN GLU ASP GLY SER PHE PHE SEQRES 7 A 356 VAL LEU THR ASN MET ILE ILE THR THR ASN GLN THR GLN SEQRES 8 A 356 SER LYS CYS ALA GLU ASN PRO THR PRO ALA SER THR CYS SEQRES 9 A 356 THR SER HIS ARG ASP CYS LYS ARG GLY PHE ASN ASP ALA SEQRES 10 A 356 ARG GLY ASP GLY VAL ARG THR GLY ARG CYS VAL SER TYR SEQRES 11 A 356 SER ALA SER VAL LYS THR CYS GLU VAL LEU SER TRP CYS SEQRES 12 A 356 PRO LEU GLU LYS ILE VAL ASP PRO PRO ASN PRO PRO LEU SEQRES 13 A 356 LEU ALA ASP ALA GLU ARG PHE THR VAL LEU ILE LYS ASN SEQRES 14 A 356 ASN ILE ARG TYR PRO LYS PHE ASN PHE ASN LYS ARG ASN SEQRES 15 A 356 ILE LEU PRO ASN ILE ASN SER SER TYR LEU THR HIS CYS SEQRES 16 A 356 VAL PHE SER ARG LYS THR ASP PRO ASP CYS PRO ILE PHE SEQRES 17 A 356 ARG LEU GLY ASP ILE VAL GLY GLU ALA GLU GLU ASP PHE SEQRES 18 A 356 GLN ILE MET ALA VAL ARG GLY GLY VAL MET GLY VAL GLN SEQRES 19 A 356 ILE ARG TRP ASP CYS ASP LEU ASP MET PRO GLN SER TRP SEQRES 20 A 356 CYS VAL PRO ARG TYR THR PHE ARG ARG LEU ASP ASN LYS SEQRES 21 A 356 ASP PRO ASP ASN ASN VAL ALA PRO GLY TYR ASN PHE ARG SEQRES 22 A 356 PHE ALA LYS TYR TYR LYS ASN SER ASP GLY THR GLU THR SEQRES 23 A 356 ARG THR LEU ILE LYS GLY TYR GLY ILE ARG PHE ASP VAL SEQRES 24 A 356 MET VAL PHE GLY GLN ALA GLY LYS PHE ASN ILE ILE PRO SEQRES 25 A 356 THR LEU LEU ASN ILE GLY ALA GLY LEU ALA LEU LEU GLY SEQRES 26 A 356 LEU VAL ASN VAL ILE CYS ASP TRP ILE VAL LEU THR PHE SEQRES 27 A 356 MET LYS ARG LYS GLN HIS TYR LYS GLU GLN LYS TYR THR SEQRES 28 A 356 TYR VAL ASP ASP PHE MODRES 3H9V ASN A 113 ASN GLYCOSYLATION SITE MODRES 3H9V ASN A 213 ASN GLYCOSYLATION SITE HET NAG B 1 14 HET NAG B 2 14 HET NAG C 1 14 HET NAG C 2 14 HET GD A 382 1 HET GD A 383 1 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM GD GADOLINIUM ATOM HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE FORMUL 2 NAG 4(C8 H15 N O6) FORMUL 4 GD 2(GD) HELIX 1 1 GLY A 32 ILE A 47 1 16 HELIX 2 2 ASN A 140 GLY A 144 5 5 HELIX 3 3 LEU A 182 ARG A 187 5 6 HELIX 4 4 SER A 215 HIS A 219 5 5 HELIX 5 5 LEU A 235 ALA A 242 1 8 HELIX 6 6 ASP A 245 VAL A 251 1 7 HELIX 7 7 ASN A 334 VAL A 360 1 27 SHEET 1 A 3 LEU A 64 LYS A 72 0 SHEET 2 A 3 THR A 189 TYR A 198 -1 O ARG A 197 N LEU A 64 SHEET 3 A 3 PHE A 203 ARG A 206 -1 O PHE A 203 N TYR A 198 SHEET 1 B 3 LEU A 64 LYS A 72 0 SHEET 2 B 3 THR A 189 TYR A 198 -1 O ARG A 197 N LEU A 64 SHEET 3 B 3 ILE A 232 ARG A 234 -1 O PHE A 233 N VAL A 190 SHEET 1 C 2 ILE A 74 THR A 79 0 SHEET 2 C 2 GLY A 83 ASP A 88 -1 O ARG A 85 N THR A 77 SHEET 1 D 4 PHE A 102 GLN A 114 0 SHEET 2 D 4 GLU A 310 PHE A 327 -1 O PHE A 322 N PHE A 102 SHEET 3 D 4 GLY A 254 ASP A 265 1 N VAL A 258 O ASP A 323 SHEET 4 D 4 ASN A 296 LYS A 304 0 SHEET 1 E 4 VAL A 274 ARG A 281 0 SHEET 2 E 4 GLY A 254 ASP A 265 -1 N GLY A 257 O ARG A 280 SHEET 3 E 4 GLU A 310 PHE A 327 1 O ASP A 323 N VAL A 258 SHEET 4 E 4 ALA A 330 GLY A 331 0 SHEET 1 F 3 SER A 117 ALA A 120 0 SHEET 2 F 3 THR A 161 SER A 166 -1 O SER A 166 N SER A 117 SHEET 3 F 3 VAL A 147 VAL A 153 -1 N VAL A 153 O THR A 161 SSBOND 1 CYS A 119 CYS A 168 1555 1555 2.04 SSBOND 2 CYS A 129 CYS A 152 1555 1555 2.03 SSBOND 3 CYS A 135 CYS A 162 1555 1555 2.04 SSBOND 4 CYS A 220 CYS A 230 1555 1555 2.04 SSBOND 5 CYS A 264 CYS A 273 1555 1555 2.06 LINK ND2 ASN A 113 C1 NAG B 1 1555 1555 1.45 LINK ND2 ASN A 213 C1 NAG C 1 1555 1555 1.43 LINK O4 NAG B 1 C1 NAG B 2 1555 1555 1.50 LINK O4 NAG C 1 C1 NAG C 2 1555 1555 1.44 CISPEP 1 PRO A 95 PRO A 96 0 -11.77 CISPEP 2 CYS A 168 PRO A 169 0 -0.81 CISPEP 3 ASN A 178 PRO A 179 0 3.97 CRYST1 100.836 100.836 431.316 90.00 90.00 120.00 H 3 2 18 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 0.009917 0.005726 0.000000 0.00000 SCALE2 0.000000 0.011451 0.000000 0.00000 SCALE3 0.000000 0.000000 0.002318 0.00000