HEADER HYDROLASE 16-JUL-15 5CLQ TITLE RAN Y39A IN COMPLEX WITH GPPNHP AND RANBD1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: GTP-BINDING NUCLEAR PROTEIN RAN; COMPND 3 CHAIN: A, C; COMPND 4 SYNONYM: ANDROGEN RECEPTOR-ASSOCIATED PROTEIN 24,GTPASE RAN,RAS-LIKE COMPND 5 PROTEIN TC4,RAS-RELATED NUCLEAR PROTEIN; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: E3 SUMO-PROTEIN LIGASE RANBP2; COMPND 10 CHAIN: B, D; COMPND 11 FRAGMENT: RAN BINDING DOMAIN 1, UNP RESIDUES 1155-1321; COMPND 12 SYNONYM: 358 KDA NUCLEOPORIN,NUCLEAR PORE COMPLEX PROTEIN NUP358, COMPND 13 NUCLEOPORIN NUP358,RAN-BINDING PROTEIN 2,RANBP2,P270; COMPND 14 EC: 6.3.2.-; COMPND 15 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: RAN, ARA24, OK/SW-CL.81; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET3D; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606; SOURCE 13 GENE: RANBP2, NUP358; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 15 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 16 EXPRESSION_SYSTEM_PLASMID: PGEX4T1 KEYWDS GTPASE, NUCLEAR TRANSPORT, HYDROLASE, RAN BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR I.R.VETTER,S.BRUCKER REVDAT 3 10-JAN-24 5CLQ 1 LINK REVDAT 2 14-OCT-15 5CLQ 1 JRNL REVDAT 1 09-SEP-15 5CLQ 0 JRNL AUTH T.RUDACK,S.JENRICH,S.BRUCKER,I.R.VETTER,K.GERWERT,C.KOTTING JRNL TITL CATALYSIS OF GTP HYDROLYSIS BY SMALL GTPASES AT ATOMIC JRNL TITL 2 DETAIL BY INTEGRATION OF X-RAY CRYSTALLOGRAPHY, JRNL TITL 3 EXPERIMENTAL, AND THEORETICAL IR SPECTROSCOPY. JRNL REF J.BIOL.CHEM. V. 290 24079 2015 JRNL REFN ESSN 1083-351X JRNL PMID 26272610 JRNL DOI 10.1074/JBC.M115.648071 REMARK 2 REMARK 2 RESOLUTION. 3.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.4_1496 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) : 3.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.98 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 19894 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.225 REMARK 3 R VALUE (WORKING SET) : 0.224 REMARK 3 FREE R VALUE : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 995 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 19.9839 - 6.0720 1.00 2809 148 0.2040 0.2127 REMARK 3 2 6.0720 - 4.8421 1.00 2718 143 0.2157 0.2569 REMARK 3 3 4.8421 - 4.2367 1.00 2705 143 0.1988 0.2349 REMARK 3 4 4.2367 - 3.8524 1.00 2678 140 0.2284 0.2834 REMARK 3 5 3.8524 - 3.5779 1.00 2673 138 0.2491 0.2738 REMARK 3 6 3.5779 - 3.3680 1.00 2660 141 0.2675 0.3168 REMARK 3 7 3.3680 - 3.2001 1.00 2656 142 0.2981 0.3373 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) : 0.310 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.490 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 : 0.010 5637 REMARK 3 ANGLE : 2.005 7633 REMARK 3 CHIRALITY : 0.085 824 REMARK 3 PLANARITY : 0.009 967 REMARK 3 DIHEDRAL : 23.638 3451 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 5CLQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-JUL-15. REMARK 100 THE DEPOSITION ID IS D_1000211833. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-MAY-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X10SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0039 REMARK 200 MONOCHROMATOR : SI(111) MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19912 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.200 REMARK 200 RESOLUTION RANGE LOW (A) : 87.924 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 6.560 REMARK 200 R MERGE (I) : 0.09400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.9900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 6.87 REMARK 200 R MERGE FOR SHELL (I) : 0.87100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.970 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: 1RRP REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 64.22 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.44 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.8M AMMONIUM SULFATE, 2.5% PEG 1500, REMARK 280 100 MM HEPES PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 67.82500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 67.82500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 51.26500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 85.46000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 51.26500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 85.46000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 67.82500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 51.26500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 85.46000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 67.82500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 51.26500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 85.46000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5740 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17190 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -70.0 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5840 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16240 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -73.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D 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 1 REMARK 465 ALA A 2 REMARK 465 ALA A 3 REMARK 465 GLN A 4 REMARK 465 GLU A 212 REMARK 465 ASP A 213 REMARK 465 ASP A 214 REMARK 465 ASP A 215 REMARK 465 LEU A 216 REMARK 465 GLU B 1 REMARK 465 THR B 2 REMARK 465 ASP B 3 REMARK 465 GLY B 4 REMARK 465 GLY B 5 REMARK 465 SER B 6 REMARK 465 ALA B 7 REMARK 465 HIS B 8 REMARK 465 GLY B 9 REMARK 465 ASP B 10 REMARK 465 ASP B 11 REMARK 465 ASP B 12 REMARK 465 ASP B 13 REMARK 465 ASP B 14 REMARK 465 GLY B 15 REMARK 465 PRO B 16 REMARK 465 HIS B 17 REMARK 465 PHE B 18 REMARK 465 ALA B 153 REMARK 465 PRO B 154 REMARK 465 GLY B 155 REMARK 465 THR B 156 REMARK 465 ASN B 157 REMARK 465 VAL B 158 REMARK 465 ALA B 159 REMARK 465 MET B 160 REMARK 465 ALA B 161 REMARK 465 SER B 162 REMARK 465 ASN B 163 REMARK 465 GLN B 164 REMARK 465 ALA B 165 REMARK 465 VAL B 166 REMARK 465 ARG B 167 REMARK 465 MET C 1 REMARK 465 ALA C 2 REMARK 465 ALA C 3 REMARK 465 GLN C 4 REMARK 465 GLY C 5 REMARK 465 GLU C 6 REMARK 465 PRO C 7 REMARK 465 ARG C 140 REMARK 465 LYS C 141 REMARK 465 LYS C 142 REMARK 465 ASN C 143 REMARK 465 GLU C 212 REMARK 465 ASP C 213 REMARK 465 ASP C 214 REMARK 465 ASP C 215 REMARK 465 LEU C 216 REMARK 465 GLU D 1 REMARK 465 THR D 2 REMARK 465 ASP D 3 REMARK 465 GLY D 4 REMARK 465 GLY D 5 REMARK 465 SER D 6 REMARK 465 ALA D 7 REMARK 465 HIS D 8 REMARK 465 GLY D 9 REMARK 465 ASP D 10 REMARK 465 ASP D 11 REMARK 465 ASP D 12 REMARK 465 ASP D 13 REMARK 465 ASP D 14 REMARK 465 GLY D 15 REMARK 465 PRO D 16 REMARK 465 HIS D 17 REMARK 465 PHE D 18 REMARK 465 GLU D 19 REMARK 465 PRO D 20 REMARK 465 VAL D 21 REMARK 465 ALA D 153 REMARK 465 PRO D 154 REMARK 465 GLY D 155 REMARK 465 THR D 156 REMARK 465 ASN D 157 REMARK 465 VAL D 158 REMARK 465 ALA D 159 REMARK 465 MET D 160 REMARK 465 ALA D 161 REMARK 465 SER D 162 REMARK 465 ASN D 163 REMARK 465 GLN D 164 REMARK 465 ALA D 165 REMARK 465 VAL D 166 REMARK 465 ARG D 167 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 TRP C 163 NZ LYS C 167 2.09 REMARK 500 NH2 ARG D 60 OD2 ASP D 119 2.14 REMARK 500 N THR D 32 OE2 GLU D 35 2.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 ASP D 26 CB ASP D 26 CG 0.129 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 LEU A 75 CA - CB - CG ANGL. DEV. = 15.8 DEGREES REMARK 500 HIS A 199 CB - CA - C ANGL. DEV. = 12.7 DEGREES REMARK 500 PRO B 23 C - N - CA ANGL. DEV. = 9.1 DEGREES REMARK 500 LEU B 121 CB - CG - CD2 ANGL. DEV. = -12.7 DEGREES REMARK 500 ARG C 56 NE - CZ - NH1 ANGL. DEV. = -3.5 DEGREES REMARK 500 GLY C 170 N - CA - C ANGL. DEV. = 23.3 DEGREES REMARK 500 ASP C 171 CB - CG - OD1 ANGL. DEV. = -5.7 DEGREES REMARK 500 ASP C 171 CB - CG - OD2 ANGL. DEV. = 5.7 DEGREES REMARK 500 PRO C 172 C - N - CA ANGL. DEV. = 11.1 DEGREES REMARK 500 ASP D 26 N - CA - CB ANGL. DEV. = 12.4 DEGREES REMARK 500 GLU D 38 CB - CA - C ANGL. DEV. = -12.7 DEGREES REMARK 500 GLU D 38 CA - CB - CG ANGL. DEV. = 13.5 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 GLU A 113 -75.16 -58.98 REMARK 500 ASN A 114 56.84 -92.58 REMARK 500 ARG A 140 -43.51 -28.70 REMARK 500 ASN A 154 -1.33 67.88 REMARK 500 ASN A 156 17.78 50.08 REMARK 500 ALA A 204 -73.63 -71.23 REMARK 500 GLN A 205 -10.60 -47.69 REMARK 500 GLN B 84 -51.51 74.67 REMARK 500 ASN B 91 97.40 -162.76 REMARK 500 ALA B 104 -114.47 36.89 REMARK 500 GLU C 113 -79.89 -58.43 REMARK 500 ASN C 114 58.55 -93.84 REMARK 500 LYS C 123 31.35 71.60 REMARK 500 ASN C 154 -2.34 68.91 REMARK 500 ASN C 156 18.37 49.29 REMARK 500 ASP C 171 146.54 163.15 REMARK 500 VAL C 188 -169.95 -102.22 REMARK 500 ALA C 204 -74.84 -71.93 REMARK 500 GLN C 205 -10.35 -48.57 REMARK 500 ALA C 208 145.43 -38.42 REMARK 500 GLN D 84 -51.25 73.47 REMARK 500 ASN D 91 96.54 -162.64 REMARK 500 ALA D 104 -117.18 33.06 REMARK 500 GLU D 120 -3.62 62.11 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ASP C 171 PRO C 172 -130.41 REMARK 500 ASP D 26 LYS D 27 -118.04 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 LYS D 27 10.87 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 MG A 302 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 24 OG1 REMARK 620 2 THR A 42 OG1 64.1 REMARK 620 3 GNP A 301 O2G 124.9 79.4 REMARK 620 4 GNP A 301 O1B 86.3 122.5 80.0 REMARK 620 5 HOH A 401 O 72.1 68.6 56.2 55.4 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG C 303 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR C 24 OG1 REMARK 620 2 THR C 42 OG1 89.4 REMARK 620 3 GNP C 302 O2G 163.3 85.2 REMARK 620 4 GNP C 302 O2B 89.6 164.1 91.3 REMARK 620 5 HOH C 402 O 92.9 93.3 71.7 71.0 REMARK 620 6 HOH C 404 O 104.5 95.4 91.8 100.2 160.7 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GNP A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 C 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GNP C 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG C 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 D 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 D 202 DBREF 5CLQ A 1 216 UNP P62826 RAN_HUMAN 1 216 DBREF 5CLQ B 1 167 UNP P49792 RBP2_HUMAN 1155 1321 DBREF 5CLQ C 1 216 UNP P62826 RAN_HUMAN 1 216 DBREF 5CLQ D 1 167 UNP P49792 RBP2_HUMAN 1155 1321 SEQADV 5CLQ ALA A 39 UNP P62826 TYR 39 ENGINEERED MUTATION SEQADV 5CLQ ALA C 39 UNP P62826 TYR 39 ENGINEERED MUTATION SEQRES 1 A 216 MET ALA ALA GLN GLY GLU PRO GLN VAL GLN PHE LYS LEU SEQRES 2 A 216 VAL LEU VAL GLY ASP GLY GLY THR GLY LYS THR THR PHE SEQRES 3 A 216 VAL LYS ARG HIS LEU THR GLY GLU PHE GLU LYS LYS ALA SEQRES 4 A 216 VAL ALA THR LEU GLY VAL GLU VAL HIS PRO LEU VAL PHE SEQRES 5 A 216 HIS THR ASN ARG GLY PRO ILE LYS PHE ASN VAL TRP ASP SEQRES 6 A 216 THR ALA GLY GLN GLU LYS PHE GLY GLY LEU ARG ASP GLY SEQRES 7 A 216 TYR TYR ILE GLN ALA GLN CYS ALA ILE ILE MET PHE ASP SEQRES 8 A 216 VAL THR SER ARG VAL THR TYR LYS ASN VAL PRO ASN TRP SEQRES 9 A 216 HIS ARG ASP LEU VAL ARG VAL CYS GLU ASN ILE PRO ILE SEQRES 10 A 216 VAL LEU CYS GLY ASN LYS VAL ASP ILE LYS ASP ARG LYS SEQRES 11 A 216 VAL LYS ALA LYS SER ILE VAL PHE HIS ARG LYS LYS ASN SEQRES 12 A 216 LEU GLN TYR TYR ASP ILE SER ALA LYS SER ASN TYR ASN SEQRES 13 A 216 PHE GLU LYS PRO PHE LEU TRP LEU ALA ARG LYS LEU ILE SEQRES 14 A 216 GLY ASP PRO ASN LEU GLU PHE VAL ALA MET PRO ALA LEU SEQRES 15 A 216 ALA PRO PRO GLU VAL VAL MET ASP PRO ALA LEU ALA ALA SEQRES 16 A 216 GLN TYR GLU HIS ASP LEU GLU VAL ALA GLN THR THR ALA SEQRES 17 A 216 LEU PRO ASP GLU ASP ASP ASP LEU SEQRES 1 B 167 GLU THR ASP GLY GLY SER ALA HIS GLY ASP ASP ASP ASP SEQRES 2 B 167 ASP GLY PRO HIS PHE GLU PRO VAL VAL PRO LEU PRO ASP SEQRES 3 B 167 LYS ILE GLU VAL LYS THR GLY GLU GLU ASP GLU GLU GLU SEQRES 4 B 167 PHE PHE CYS ASN ARG ALA LYS LEU PHE ARG PHE ASP VAL SEQRES 5 B 167 GLU SER LYS GLU TRP LYS GLU ARG GLY ILE GLY ASN VAL SEQRES 6 B 167 LYS ILE LEU ARG HIS LYS THR SER GLY LYS ILE ARG LEU SEQRES 7 B 167 LEU MET ARG ARG GLU GLN VAL LEU LYS ILE CYS ALA ASN SEQRES 8 B 167 HIS TYR ILE SER PRO ASP MET LYS LEU THR PRO ASN ALA SEQRES 9 B 167 GLY SER ASP ARG SER PHE VAL TRP HIS ALA LEU ASP TYR SEQRES 10 B 167 ALA ASP GLU LEU PRO LYS PRO GLU GLN LEU ALA ILE ARG SEQRES 11 B 167 PHE LYS THR PRO GLU GLU ALA ALA LEU PHE LYS CYS LYS SEQRES 12 B 167 PHE GLU GLU ALA GLN SER ILE LEU LYS ALA PRO GLY THR SEQRES 13 B 167 ASN VAL ALA MET ALA SER ASN GLN ALA VAL ARG SEQRES 1 C 216 MET ALA ALA GLN GLY GLU PRO GLN VAL GLN PHE LYS LEU SEQRES 2 C 216 VAL LEU VAL GLY ASP GLY GLY THR GLY LYS THR THR PHE SEQRES 3 C 216 VAL LYS ARG HIS LEU THR GLY GLU PHE GLU LYS LYS ALA SEQRES 4 C 216 VAL ALA THR LEU GLY VAL GLU VAL HIS PRO LEU VAL PHE SEQRES 5 C 216 HIS THR ASN ARG GLY PRO ILE LYS PHE ASN VAL TRP ASP SEQRES 6 C 216 THR ALA GLY GLN GLU LYS PHE GLY GLY LEU ARG ASP GLY SEQRES 7 C 216 TYR TYR ILE GLN ALA GLN CYS ALA ILE ILE MET PHE ASP SEQRES 8 C 216 VAL THR SER ARG VAL THR TYR LYS ASN VAL PRO ASN TRP SEQRES 9 C 216 HIS ARG ASP LEU VAL ARG VAL CYS GLU ASN ILE PRO ILE SEQRES 10 C 216 VAL LEU CYS GLY ASN LYS VAL ASP ILE LYS ASP ARG LYS SEQRES 11 C 216 VAL LYS ALA LYS SER ILE VAL PHE HIS ARG LYS LYS ASN SEQRES 12 C 216 LEU GLN TYR TYR ASP ILE SER ALA LYS SER ASN TYR ASN SEQRES 13 C 216 PHE GLU LYS PRO PHE LEU TRP LEU ALA ARG LYS LEU ILE SEQRES 14 C 216 GLY ASP PRO ASN LEU GLU PHE VAL ALA MET PRO ALA LEU SEQRES 15 C 216 ALA PRO PRO GLU VAL VAL MET ASP PRO ALA LEU ALA ALA SEQRES 16 C 216 GLN TYR GLU HIS ASP LEU GLU VAL ALA GLN THR THR ALA SEQRES 17 C 216 LEU PRO ASP GLU ASP ASP ASP LEU SEQRES 1 D 167 GLU THR ASP GLY GLY SER ALA HIS GLY ASP ASP ASP ASP SEQRES 2 D 167 ASP GLY PRO HIS PHE GLU PRO VAL VAL PRO LEU PRO ASP SEQRES 3 D 167 LYS ILE GLU VAL LYS THR GLY GLU GLU ASP GLU GLU GLU SEQRES 4 D 167 PHE PHE CYS ASN ARG ALA LYS LEU PHE ARG PHE ASP VAL SEQRES 5 D 167 GLU SER LYS GLU TRP LYS GLU ARG GLY ILE GLY ASN VAL SEQRES 6 D 167 LYS ILE LEU ARG HIS LYS THR SER GLY LYS ILE ARG LEU SEQRES 7 D 167 LEU MET ARG ARG GLU GLN VAL LEU LYS ILE CYS ALA ASN SEQRES 8 D 167 HIS TYR ILE SER PRO ASP MET LYS LEU THR PRO ASN ALA SEQRES 9 D 167 GLY SER ASP ARG SER PHE VAL TRP HIS ALA LEU ASP TYR SEQRES 10 D 167 ALA ASP GLU LEU PRO LYS PRO GLU GLN LEU ALA ILE ARG SEQRES 11 D 167 PHE LYS THR PRO GLU GLU ALA ALA LEU PHE LYS CYS LYS SEQRES 12 D 167 PHE GLU GLU ALA GLN SER ILE LEU LYS ALA PRO GLY THR SEQRES 13 D 167 ASN VAL ALA MET ALA SER ASN GLN ALA VAL ARG HET GNP A 301 32 HET MG A 302 1 HET SO4 A 303 5 HET SO4 A 304 5 HET SO4 B 201 5 HET SO4 C 301 5 HET GNP C 302 32 HET MG C 303 1 HET SO4 D 201 5 HET SO4 D 202 5 HETNAM GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER HETNAM MG MAGNESIUM ION HETNAM SO4 SULFATE ION FORMUL 5 GNP 2(C10 H17 N6 O13 P3) FORMUL 6 MG 2(MG 2+) FORMUL 7 SO4 6(O4 S 2-) FORMUL 15 HOH *12(H2 O) HELIX 1 AA1 GLY A 22 GLY A 33 1 12 HELIX 2 AA2 LEU A 75 TYR A 80 1 6 HELIX 3 AA3 SER A 94 ASN A 100 1 7 HELIX 4 AA4 ASN A 100 ARG A 110 1 11 HELIX 5 AA5 LYS A 132 ILE A 136 5 5 HELIX 6 AA6 VAL A 137 LYS A 141 5 5 HELIX 7 AA7 GLU A 158 GLY A 170 1 13 HELIX 8 AA8 LEU A 193 THR A 206 1 14 HELIX 9 AA9 THR B 133 ILE B 150 1 18 HELIX 10 AB1 GLY C 22 GLY C 33 1 12 HELIX 11 AB2 SER C 94 ASN C 100 1 7 HELIX 12 AB3 ASN C 100 ARG C 110 1 11 HELIX 13 AB4 LYS C 132 ILE C 136 5 5 HELIX 14 AB5 GLU C 158 GLY C 170 1 13 HELIX 15 AB6 LEU C 193 THR C 206 1 14 HELIX 16 AB7 THR D 133 SER D 149 1 17 SHEET 1 AA1 6 VAL A 45 THR A 54 0 SHEET 2 AA1 6 GLY A 57 THR A 66 -1 O PHE A 61 N LEU A 50 SHEET 3 AA1 6 GLN A 10 GLY A 17 1 N LEU A 13 O TRP A 64 SHEET 4 AA1 6 CYS A 85 ASP A 91 1 O MET A 89 N VAL A 16 SHEET 5 AA1 6 ILE A 117 ASN A 122 1 O VAL A 118 N ILE A 88 SHEET 6 AA1 6 LEU A 144 ASP A 148 1 O GLN A 145 N LEU A 119 SHEET 1 AA2 7 ILE B 88 TYR B 93 0 SHEET 2 AA2 7 ILE B 76 ARG B 82 -1 N LEU B 78 O HIS B 92 SHEET 3 AA2 7 GLU B 56 HIS B 70 -1 N LEU B 68 O ARG B 77 SHEET 4 AA2 7 GLU B 37 ASP B 51 -1 N PHE B 40 O ILE B 67 SHEET 5 AA2 7 LYS B 123 ARG B 130 -1 O GLN B 126 N PHE B 50 SHEET 6 AA2 7 SER B 109 ASP B 116 -1 N TRP B 112 O LEU B 127 SHEET 7 AA2 7 THR B 101 PRO B 102 -1 N THR B 101 O VAL B 111 SHEET 1 AA3 6 VAL C 45 THR C 54 0 SHEET 2 AA3 6 GLY C 57 THR C 66 -1 O ASP C 65 N GLU C 46 SHEET 3 AA3 6 VAL C 9 VAL C 16 1 N LEU C 13 O TRP C 64 SHEET 4 AA3 6 CYS C 85 ASP C 91 1 O MET C 89 N VAL C 16 SHEET 5 AA3 6 ILE C 117 ASN C 122 1 O VAL C 118 N ILE C 88 SHEET 6 AA3 6 GLN C 145 ASP C 148 1 O TYR C 147 N GLY C 121 SHEET 1 AA4 7 ILE D 88 TYR D 93 0 SHEET 2 AA4 7 ILE D 76 ARG D 81 -1 N LEU D 78 O HIS D 92 SHEET 3 AA4 7 GLU D 56 ARG D 69 -1 N LYS D 66 O LEU D 79 SHEET 4 AA4 7 GLU D 39 ASP D 51 -1 N LEU D 47 O GLY D 61 SHEET 5 AA4 7 LYS D 123 ARG D 130 -1 O ALA D 128 N PHE D 48 SHEET 6 AA4 7 SER D 109 ASP D 116 -1 N TRP D 112 O LEU D 127 SHEET 7 AA4 7 THR D 101 PRO D 102 -1 N THR D 101 O VAL D 111 SSBOND 1 CYS B 142 CYS B 142 1555 4565 2.02 SSBOND 2 CYS D 142 CYS D 142 1555 3654 2.03 LINK OG1 THR A 24 MG MG A 302 1555 1555 2.03 LINK OG1 THR A 42 MG MG A 302 1555 1555 2.14 LINK O2G GNP A 301 MG MG A 302 1555 1555 2.16 LINK O1B GNP A 301 MG MG A 302 1555 1555 2.11 LINK MG MG A 302 O HOH A 401 1555 1555 2.72 LINK OG1 THR C 24 MG MG C 303 1555 1555 1.94 LINK OG1 THR C 42 MG MG C 303 1555 1555 1.99 LINK O2G GNP C 302 MG MG C 303 1555 1555 1.98 LINK O2B GNP C 302 MG MG C 303 1555 1555 2.11 LINK MG MG C 303 O HOH C 402 1555 1555 2.31 LINK MG MG C 303 O HOH C 404 1555 1555 2.03 CISPEP 1 VAL D 22 PRO D 23 0 -14.11 CISPEP 2 LEU D 151 LYS D 152 0 26.52 SITE 1 AC1 25 ASP A 18 GLY A 19 GLY A 20 THR A 21 SITE 2 AC1 25 GLY A 22 LYS A 23 THR A 24 THR A 25 SITE 3 AC1 25 GLU A 36 LYS A 37 LYS A 38 ALA A 39 SITE 4 AC1 25 ALA A 41 THR A 42 ALA A 67 GLY A 68 SITE 5 AC1 25 ASN A 122 LYS A 123 ASP A 125 ILE A 126 SITE 6 AC1 25 SER A 150 ALA A 151 LYS A 152 MG A 302 SITE 7 AC1 25 HOH A 401 SITE 1 AC2 4 THR A 24 THR A 42 GNP A 301 HOH A 401 SITE 1 AC3 3 PRO A 102 PHE A 138 ARG A 140 SITE 1 AC4 1 GLU C 70 SITE 1 AC5 2 ARG B 49 ASP B 119 SITE 1 AC6 3 TYR A 147 ARG A 166 LYS C 37 SITE 1 AC7 24 GLY C 19 GLY C 20 THR C 21 GLY C 22 SITE 2 AC7 24 LYS C 23 THR C 24 THR C 25 GLU C 36 SITE 3 AC7 24 LYS C 37 LYS C 38 ALA C 39 ALA C 41 SITE 4 AC7 24 THR C 42 GLY C 68 ASN C 122 LYS C 123 SITE 5 AC7 24 ASP C 125 ILE C 126 ALA C 151 LYS C 152 SITE 6 AC7 24 MG C 303 HOH C 401 HOH C 402 HOH C 404 SITE 1 AC8 5 THR C 24 THR C 42 GNP C 302 HOH C 402 SITE 2 AC8 5 HOH C 404 SITE 1 AC9 4 GLY D 105 SER D 106 ASP D 107 ARG D 108 SITE 1 AD1 3 ASN D 64 LYS D 66 ARG D 81 CRYST1 102.530 170.920 135.650 90.00 90.00 90.00 C 2 2 21 16 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 0.009753 0.000000 0.000000 0.00000 SCALE2 0.000000 0.005851 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007372 0.00000