HEADER MEMBRANE PROTEIN 20-DEC-10 3Q2R TITLE CRYSTAL STRUCTURE OF SGLIPR1 SOAKED WITH ZINC CHLORIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLIOMA PATHOGENESIS-RELATED PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 22-220; COMPND 5 SYNONYM: GLIPR 1, PROTEIN RTVP-1; COMPND 6 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: GLIPR, GLIPR1, RTVP1, SYNTHESIZED; SOURCE 6 EXPRESSION_SYSTEM: PICHIA PASTORIS; SOURCE 7 EXPRESSION_SYSTEM_COMMON: YEAST; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 4922; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: X33; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PPICZALPHA KEYWDS GLIOMA, CRISP, HUMAN GLIOMA PATHOGENESIS-RELATED PROTEIN 1 (GLIPR1), KEYWDS 2 RTVP1, MEMBRANE PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR O.A.ASOJO REVDAT 4 13-SEP-23 3Q2R 1 REMARK SEQADV LINK REVDAT 3 17-JUL-19 3Q2R 1 REMARK REVDAT 2 08-NOV-17 3Q2R 1 REMARK REVDAT 1 05-OCT-11 3Q2R 0 JRNL AUTH O.A.ASOJO,R.A.KOSKI,N.BONAFE JRNL TITL STRUCTURAL STUDIES OF HUMAN GLIOMA PATHOGENESIS-RELATED JRNL TITL 2 PROTEIN 1. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 67 847 2011 JRNL REFN ISSN 0907-4449 JRNL PMID 21931216 JRNL DOI 10.1107/S0907444911028198 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX DEV_777 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.79 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 14042 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.160 REMARK 3 R VALUE (WORKING SET) : 0.158 REMARK 3 FREE R VALUE : 0.192 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 703 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 27.7904 - 3.7595 0.99 2822 127 0.1989 0.1927 REMARK 3 2 3.7595 - 2.9852 1.00 2664 134 0.1468 0.2013 REMARK 3 3 2.9852 - 2.6081 1.00 2628 151 0.1421 0.1658 REMARK 3 4 2.6081 - 2.3698 1.00 2625 149 0.1405 0.1966 REMARK 3 5 2.3698 - 2.2000 1.00 2600 142 0.1462 0.2047 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 0.90 REMARK 3 SHRINKAGE RADIUS : 0.61 REMARK 3 K_SOL : 0.42 REMARK 3 B_SOL : 38.50 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.350 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.090 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) : -2.05290 REMARK 3 B22 (A**2) : -1.02310 REMARK 3 B33 (A**2) : -0.64120 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 : 0.007 1588 REMARK 3 ANGLE : 0.982 2157 REMARK 3 CHIRALITY : 0.071 225 REMARK 3 PLANARITY : 0.004 282 REMARK 3 DIHEDRAL : 12.974 569 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3Q2R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-JAN-11. REMARK 100 THE DEPOSITION ID IS D_1000063120. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-DEC-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : SEALED TUBE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : OXFORD DIFFRACTION ENHANCE ULTRA REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.514 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : OXFORD ONYX CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSALISPRO REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18698 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 27.790 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 5.800 REMARK 200 R MERGE (I) : 0.17900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.10 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.1 REMARK 200 DATA REDUNDANCY IN SHELL : 4.50 REMARK 200 R MERGE FOR SHELL (I) : 0.62100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.500 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: 1RC9 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.78 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.85 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.085M SODIUM CACODYLATE, 25.5%W/V REMARK 280 PEG8000, 0.17M AMMONIUM SULFATE, 15% GLYCEROL 0.2MM ZINC REMARK 280 CHLORIDE, PH 6.5, VAPOR DIFFUSION, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 42.96000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 39.86000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 42.96000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 39.86000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 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: MONOMERIC 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 GLU A 16 REMARK 465 ALA A 17 REMARK 465 GLU A 18 REMARK 465 ALA A 19 REMARK 465 GLU A 20 REMARK 465 PHE A 21 REMARK 465 ALA A 22 REMARK 465 LYS A 215 REMARK 465 ARG A 216 REMARK 465 TYR A 217 REMARK 465 TYR A 218 REMARK 465 SER A 219 REMARK 465 VAL A 220 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 VAL A 214 O 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 332 O HOH A 340 1.83 REMARK 500 O HOH A 321 O HOH A 368 1.88 REMARK 500 O HOH A 245 O HOH A 369 1.88 REMARK 500 OH TYR A 147 O HOH A 236 2.14 REMARK 500 O HOH A 356 O HOH A 399 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 LYS A 88 88.26 -158.44 REMARK 500 LYS A 133 -107.54 -147.53 REMARK 500 ASN A 197 -131.87 42.02 REMARK 500 ASN A 208 116.50 -167.31 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 ZN A 991 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 79 NE2 REMARK 620 2 HOH A 223 O 83.1 REMARK 620 3 HOH A 388 O 70.5 133.3 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 991 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1U53 RELATED DB: PDB REMARK 900 RELATED ID: 1RC9 RELATED DB: PDB REMARK 900 RELATED ID: 1SMB RELATED DB: PDB REMARK 900 RELATED ID: 1CFE RELATED DB: PDB REMARK 900 RELATED ID: 3Q2U RELATED DB: PDB DBREF 3Q2R A 22 220 UNP P48060 GLIP1_HUMAN 22 220 SEQADV 3Q2R GLU A 16 UNP P48060 EXPRESSION TAG SEQADV 3Q2R ALA A 17 UNP P48060 EXPRESSION TAG SEQADV 3Q2R GLU A 18 UNP P48060 EXPRESSION TAG SEQADV 3Q2R ALA A 19 UNP P48060 EXPRESSION TAG SEQADV 3Q2R GLU A 20 UNP P48060 EXPRESSION TAG SEQADV 3Q2R PHE A 21 UNP P48060 EXPRESSION TAG SEQRES 1 A 205 GLU ALA GLU ALA GLU PHE ALA ASN ILE LEU PRO ASP ILE SEQRES 2 A 205 GLU ASN GLU ASP PHE ILE LYS ASP CYS VAL ARG ILE HIS SEQRES 3 A 205 ASN LYS PHE ARG SER GLU VAL LYS PRO THR ALA SER ASP SEQRES 4 A 205 MET LEU TYR MET THR TRP ASP PRO ALA LEU ALA GLN ILE SEQRES 5 A 205 ALA LYS ALA TRP ALA SER ASN CYS GLN PHE SER HIS ASN SEQRES 6 A 205 THR ARG LEU LYS PRO PRO HIS LYS LEU HIS PRO ASN PHE SEQRES 7 A 205 THR SER LEU GLY GLU ASN ILE TRP THR GLY SER VAL PRO SEQRES 8 A 205 ILE PHE SER VAL SER SER ALA ILE THR ASN TRP TYR ASP SEQRES 9 A 205 GLU ILE GLN ASP TYR ASP PHE LYS THR ARG ILE CYS LYS SEQRES 10 A 205 LYS VAL CYS GLY HIS TYR THR GLN VAL VAL TRP ALA ASP SEQRES 11 A 205 SER TYR LYS VAL GLY CYS ALA VAL GLN PHE CYS PRO LYS SEQRES 12 A 205 VAL SER GLY PHE ASP ALA LEU SER ASN GLY ALA HIS PHE SEQRES 13 A 205 ILE CYS ASN TYR GLY PRO GLY GLY ASN TYR PRO THR TRP SEQRES 14 A 205 PRO TYR LYS ARG GLY ALA THR CYS SER ALA CYS PRO ASN SEQRES 15 A 205 ASN ASP LYS CYS LEU ASP ASN LEU CYS VAL ASN ARG GLN SEQRES 16 A 205 ARG ASP GLN VAL LYS ARG TYR TYR SER VAL HET ZN A 991 1 HETNAM ZN ZINC ION FORMUL 2 ZN ZN 2+ FORMUL 3 HOH *208(H2 O) HELIX 1 1 ASN A 30 GLU A 47 1 18 HELIX 2 2 ASP A 61 SER A 73 1 13 HELIX 3 3 SER A 109 ASP A 119 1 11 HELIX 4 4 GLU A 120 GLN A 122 5 3 HELIX 5 5 CYS A 135 VAL A 142 1 8 HELIX 6 6 ASN A 208 GLN A 213 1 6 SHEET 1 A 4 THR A 59 TRP A 60 0 SHEET 2 A 4 LYS A 148 CYS A 156 1 O VAL A 149 N THR A 59 SHEET 3 A 4 GLY A 168 GLY A 176 -1 O ASN A 174 N GLY A 150 SHEET 4 A 4 GLY A 97 SER A 104 -1 N TRP A 101 O PHE A 171 SHEET 1 B 2 TYR A 124 ASP A 125 0 SHEET 2 B 2 ILE A 130 CYS A 131 -1 O ILE A 130 N ASP A 125 SHEET 1 C 2 LYS A 200 LEU A 202 0 SHEET 2 C 2 LEU A 205 VAL A 207 -1 O LEU A 205 N LEU A 202 SSBOND 1 CYS A 75 CYS A 156 1555 1555 2.04 SSBOND 2 CYS A 131 CYS A 135 1555 1555 2.05 SSBOND 3 CYS A 151 CYS A 173 1555 1555 2.03 SSBOND 4 CYS A 192 CYS A 201 1555 1555 2.02 SSBOND 5 CYS A 195 CYS A 206 1555 1555 2.04 LINK NE2 HIS A 79 ZN ZN A 991 1555 1555 2.66 LINK O HOH A 223 ZN ZN A 991 1555 1555 2.35 LINK O HOH A 388 ZN ZN A 991 1555 1555 2.60 CISPEP 1 LYS A 49 PRO A 50 0 0.00 CISPEP 2 PRO A 85 PRO A 86 0 5.96 CISPEP 3 GLY A 176 PRO A 177 0 -12.35 SITE 1 AC1 4 HIS A 79 HIS A 137 HOH A 223 HOH A 388 CRYST1 85.920 79.720 38.760 90.00 90.00 90.00 P 21 21 2 4 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 0.011639 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012544 0.000000 0.00000 SCALE3 0.000000 0.000000 0.025800 0.00000