HEADER TRANSPORT PROTEIN 24-FEB-12 4DW0 TITLE CRYSTAL STRUCTURE OF THE ATP-GATED P2X4 ION CHANNEL IN THE CLOSED, APO TITLE 2 STATE AT 2.9 ANGSTROMS 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; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: SF9; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: BACMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PFASTBAC KEYWDS ION CHANNEL, TRANSPORT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.HATTORI,E.GOUAUX REVDAT 4 29-JUL-20 4DW0 1 COMPND REMARK SEQADV HETNAM REVDAT 4 2 1 LINK SITE ATOM REVDAT 3 09-JAN-13 4DW0 1 JRNL REVDAT 2 02-MAY-12 4DW0 1 JRNL REVDAT 1 25-APR-12 4DW0 0 JRNL AUTH M.HATTORI,E.GOUAUX JRNL TITL MOLECULAR MECHANISM OF ATP BINDING AND ION CHANNEL JRNL TITL 2 ACTIVATION IN P2X RECEPTORS. JRNL REF NATURE V. 485 207 2012 JRNL REFN ISSN 0028-0836 JRNL PMID 22535247 JRNL DOI 10.1038/NATURE11010 REMARK 2 REMARK 2 RESOLUTION. 2.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7_650) 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) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.18 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 3 NUMBER OF REFLECTIONS : 18911 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.221 REMARK 3 R VALUE (WORKING SET) : 0.220 REMARK 3 FREE R VALUE : 0.244 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.120 REMARK 3 FREE R VALUE TEST SET COUNT : 968 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 47.1901 - 5.5299 0.96 2669 141 0.2651 0.2703 REMARK 3 2 5.5299 - 4.3903 0.98 2600 141 0.1776 0.2200 REMARK 3 3 4.3903 - 3.8356 0.99 2598 133 0.1920 0.2431 REMARK 3 4 3.8356 - 3.4850 0.99 2592 135 0.1806 0.2209 REMARK 3 5 3.4850 - 3.2353 0.99 2578 148 0.2031 0.1942 REMARK 3 6 3.2353 - 3.0446 0.99 2536 155 0.2491 0.2972 REMARK 3 7 3.0446 - 2.8921 0.91 2370 115 0.3194 0.3056 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.00 REMARK 3 SHRINKAGE RADIUS : 0.72 REMARK 3 K_SOL : 0.31 REMARK 3 B_SOL : 80.00 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.410 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.410 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -25.64680 REMARK 3 B22 (A**2) : -25.64680 REMARK 3 B33 (A**2) : 51.29350 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 : 0.011 2735 REMARK 3 ANGLE : 1.385 3608 REMARK 3 CHIRALITY : 0.093 417 REMARK 3 PLANARITY : 0.006 462 REMARK 3 DIHEDRAL : 19.362 962 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: AUTHORS STATED THAT EVEN THOUGH THERE REMARK 3 IS AN APPARENT GAP IN THE LATTICE, AUTHORS KNOW THAT THERE ARE REMARK 3 STILL MANY AMINO ACID RESIDUES THAT AUTHORS HAVE NOT BEEN ABLE REMARK 3 TO MODEL IN THE STRUCTURE AND WE BELIEVE THAT THESE RESIDUES ARE REMARK 3 WHAT PROVIDE THE INTERACTIONS BETWEEN THE LAYERS REMARK 4 REMARK 4 4DW0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-FEB-12. REMARK 100 THE DEPOSITION ID IS D_1000070852. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-MAR-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 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-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97918 REMARK 200 MONOCHROMATOR : CRYO-COOLED SI(111) DOUBLE REMARK 200 CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18934 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 200 DATA REDUNDANCY : 4.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.8 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 77.74 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 5.53 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1 MM GDCL3, 20% PEG 3350, 100 MM REMARK 280 MGCL2, 2M NACL AND 100 MM IMIDAZOLE, PH 6.5, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 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 49.81300 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 28.75955 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 147.17967 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 49.81300 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 28.75955 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 147.17967 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 49.81300 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 28.75955 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 147.17967 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 49.81300 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 28.75955 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 147.17967 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 49.81300 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 28.75955 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 147.17967 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 49.81300 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 28.75955 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 147.17967 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 57.51910 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 294.35933 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 57.51910 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 294.35933 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 57.51910 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 294.35933 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 57.51910 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 294.35933 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 57.51910 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 294.35933 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 57.51910 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 294.35933 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 REMARK: THE BIOLOGICAL ASSEMBLY IS A TRIMER GENERATED FROM THE REMARK 300 PROTOMER IN THE ASYMMETRIC UNIT BY THE OPERATIONS: -Y, X-Y, Z AND Y- REMARK 300 X, -X, Z. 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: 19690 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 43010 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 22.0 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 -0.500000 -0.866025 0.000000 -49.81300 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 86.27865 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 -99.62600 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 506 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 626 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 627 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 650 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 655 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 THR A 362 REMARK 465 PHE A 363 REMARK 465 MET A 364 REMARK 465 LYS A 365 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 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 LEU A 64 CG CD1 CD2 REMARK 470 GLU A 81 CG CD OE1 OE2 REMARK 470 LEU A 82 CG CD1 CD2 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 ARG A 151 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 160 CG CD CE NZ REMARK 470 ASN A 211 CG OD1 ND2 REMARK 470 HIS A 219 CG ND1 CD2 CE1 NE2 REMARK 470 LYS A 225 CG CD CE NZ REMARK 470 LYS A 304 CG CD CE NZ 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: 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 231 C - N - CA ANGL. DEV. = 9.9 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 PHE A 51 -78.06 -105.32 REMARK 500 GLU A 81 -3.81 84.81 REMARK 500 LEU A 82 -78.11 -121.37 REMARK 500 PRO A 95 -173.93 -68.50 REMARK 500 SER A 117 -170.73 -170.44 REMARK 500 LYS A 225 -71.45 -89.09 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 GD A 506 GD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 629 O REMARK 620 2 HOH A 633 O 114.0 REMARK 620 3 HOH A 674 O 86.6 92.8 REMARK 620 N 1 2 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4DW1 RELATED DB: PDB DBREF 4DW0 A 28 365 UNP Q6NYR1 Q6NYR1_DANRE 28 365 SEQADV 4DW0 GLY A 26 UNP Q6NYR1 EXPRESSION TAG SEQADV 4DW0 SER A 27 UNP Q6NYR1 EXPRESSION TAG SEQADV 4DW0 PHE A 51 UNP Q6NYR1 CYS 51 ENGINEERED MUTATION SEQADV 4DW0 LYS A 78 UNP Q6NYR1 ASN 78 ENGINEERED MUTATION SEQADV 4DW0 ARG A 187 UNP Q6NYR1 ASN 187 ENGINEERED MUTATION SEQADV 4DW0 ARG A 252 UNP Q6NYR1 HIS 252 ENGINEERED MUTATION SEQRES 1 A 340 GLY SER SER LYS LYS VAL GLY THR LEU ASN ARG PHE THR SEQRES 2 A 340 GLN ALA LEU VAL ILE ALA TYR VAL ILE GLY TYR VAL PHE SEQRES 3 A 340 VAL TYR ASN LYS GLY TYR GLN ASP THR ASP THR VAL LEU SEQRES 4 A 340 SER SER VAL THR THR LYS VAL LYS GLY ILE ALA LEU THR SEQRES 5 A 340 LYS THR SER GLU LEU GLY GLU ARG ILE TRP ASP VAL ALA SEQRES 6 A 340 ASP TYR ILE ILE PRO PRO GLN GLU ASP GLY SER PHE PHE SEQRES 7 A 340 VAL LEU THR ASN MET ILE ILE THR THR ASN GLN THR GLN SEQRES 8 A 340 SER LYS CYS ALA GLU ASN PRO THR PRO ALA SER THR CYS SEQRES 9 A 340 THR SER HIS ARG ASP CYS LYS ARG GLY PHE ASN ASP ALA SEQRES 10 A 340 ARG GLY ASP GLY VAL ARG THR GLY ARG CYS VAL SER TYR SEQRES 11 A 340 SER ALA SER VAL LYS THR CYS GLU VAL LEU SER TRP CYS SEQRES 12 A 340 PRO LEU GLU LYS ILE VAL ASP PRO PRO ASN PRO PRO LEU SEQRES 13 A 340 LEU ALA ASP ALA GLU ARG PHE THR VAL LEU ILE LYS ASN SEQRES 14 A 340 ASN ILE ARG TYR PRO LYS PHE ASN PHE ASN LYS ARG ASN SEQRES 15 A 340 ILE LEU PRO ASN ILE ASN SER SER TYR LEU THR HIS CYS SEQRES 16 A 340 VAL PHE SER ARG LYS THR ASP PRO ASP CYS PRO ILE PHE SEQRES 17 A 340 ARG LEU GLY ASP ILE VAL GLY GLU ALA GLU GLU ASP PHE SEQRES 18 A 340 GLN ILE MET ALA VAL ARG GLY GLY VAL MET GLY VAL GLN SEQRES 19 A 340 ILE ARG TRP ASP CYS ASP LEU ASP MET PRO GLN SER TRP SEQRES 20 A 340 CYS VAL PRO ARG TYR THR PHE ARG ARG LEU ASP ASN LYS SEQRES 21 A 340 ASP PRO ASP ASN ASN VAL ALA PRO GLY TYR ASN PHE ARG SEQRES 22 A 340 PHE ALA LYS TYR TYR LYS ASN SER ASP GLY THR GLU THR SEQRES 23 A 340 ARG THR LEU ILE LYS GLY TYR GLY ILE ARG PHE ASP VAL SEQRES 24 A 340 MET VAL PHE GLY GLN ALA GLY LYS PHE ASN ILE ILE PRO SEQRES 25 A 340 THR LEU LEU ASN ILE GLY ALA GLY LEU ALA LEU LEU GLY SEQRES 26 A 340 LEU VAL ASN VAL ILE CYS ASP TRP ILE VAL LEU THR PHE SEQRES 27 A 340 MET LYS MODRES 4DW0 ASN A 113 ASN GLYCOSYLATION SITE MODRES 4DW0 ASN A 213 ASN GLYCOSYLATION SITE HET NAG B 1 14 HET NAG B 2 14 HET BMA B 3 11 HET MAN B 4 11 HET NAG A 505 14 HET GD A 506 1 HET GOL A 507 6 HET GOL A 508 6 HET GOL A 509 6 HET GOL A 510 6 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM BMA BETA-D-MANNOPYRANOSE HETNAM MAN ALPHA-D-MANNOPYRANOSE HETNAM GD GADOLINIUM ATOM HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 NAG 3(C8 H15 N O6) FORMUL 2 BMA C6 H12 O6 FORMUL 2 MAN C6 H12 O6 FORMUL 4 GD GD FORMUL 5 GOL 4(C3 H8 O3) FORMUL 9 HOH *79(H2 O) HELIX 1 1 LEU A 34 TYR A 49 1 16 HELIX 2 2 ASP A 88 ILE A 93 1 6 HELIX 3 3 LEU A 182 ARG A 187 5 6 HELIX 4 4 ASN A 213 CYS A 220 1 8 HELIX 5 5 LEU A 235 ALA A 242 1 8 HELIX 6 6 ASP A 245 ALA A 250 1 6 HELIX 7 7 PRO A 269 CYS A 273 5 5 HELIX 8 8 ASN A 334 TRP A 358 1 25 SHEET 1 A 4 GLN A 58 THR A 62 0 SHEET 2 A 4 THR A 309 PHE A 333 -1 O ALA A 330 N ASP A 61 SHEET 3 A 4 GLY A 254 ASP A 265 1 N GLY A 254 O GLY A 319 SHEET 4 A 4 PRO A 275 ARG A 281 -1 O ARG A 280 N GLY A 257 SHEET 1 B 5 VAL A 147 VAL A 153 0 SHEET 2 B 5 THR A 161 CYS A 168 -1 O THR A 161 N VAL A 153 SHEET 3 B 5 SER A 101 ALA A 120 -1 N SER A 117 O SER A 166 SHEET 4 B 5 THR A 309 PHE A 333 -1 O PHE A 322 N PHE A 102 SHEET 5 B 5 ASN A 296 ASN A 305 -1 N TYR A 303 O THR A 311 SHEET 1 C 3 LEU A 64 LYS A 72 0 SHEET 2 C 3 THR A 189 TYR A 198 -1 O THR A 189 N LYS A 72 SHEET 3 C 3 PHE A 203 ARG A 206 -1 O LYS A 205 N ILE A 196 SHEET 1 D 3 LEU A 64 LYS A 72 0 SHEET 2 D 3 THR A 189 TYR A 198 -1 O THR A 189 N LYS A 72 SHEET 3 D 3 ILE A 232 ARG A 234 -1 O PHE A 233 N VAL A 190 SHEET 1 E 2 ALA A 75 THR A 79 0 SHEET 2 E 2 GLY A 83 TRP A 87 -1 O ARG A 85 N THR A 77 SSBOND 1 CYS A 119 CYS A 168 1555 1555 2.08 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 2.03 SSBOND 5 CYS A 264 CYS A 273 1555 1555 2.04 LINK ND2 ASN A 113 C1 NAG A 505 1555 1555 1.43 LINK ND2 ASN A 213 C1 NAG B 1 1555 1555 1.45 LINK O4 NAG B 1 C1 NAG B 2 1555 1555 1.45 LINK O4 NAG B 2 C1 BMA B 3 1555 1555 1.47 LINK O3 BMA B 3 C1 MAN B 4 1555 1555 1.45 LINK GD GD A 506 O HOH A 629 1555 1555 3.06 LINK GD GD A 506 O HOH A 633 1555 1555 2.70 LINK GD GD A 506 O HOH A 674 1555 1555 2.59 CISPEP 1 ILE A 94 PRO A 95 0 -16.19 CISPEP 2 CYS A 168 PRO A 169 0 6.63 CISPEP 3 ASN A 178 PRO A 179 0 -9.41 CRYST1 99.626 99.626 441.539 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 0.010038 0.005795 0.000000 0.00000 SCALE2 0.000000 0.011590 0.000000 0.00000 SCALE3 0.000000 0.000000 0.002265 0.00000