HEADER SIGNALING PROTEIN 21-NOV-14 4D7C TITLE MONOCLINIC CRYSTAL FORM OF THE EXTRACELLULAR OLFACTOMEDIN DOMAIN FROM TITLE 2 GLIOMEDIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLIOMEDIN; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: OLFACTOMEDIN DOMAIN, UNP RESIDUES 260-543; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: NORWAY RAT; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 6 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS KEYWDS SIGNALING PROTEIN, MYELIN, BETA-PROPELLER EXPDTA X-RAY DIFFRACTION AUTHOR H.HAN,P.KURSULA REVDAT 4 20-DEC-23 4D7C 1 REMARK LINK REVDAT 3 04-MAR-15 4D7C 1 JRNL REVDAT 2 31-DEC-14 4D7C 1 JRNL REVDAT 1 24-DEC-14 4D7C 0 JRNL AUTH H.HAN,P.KURSULA JRNL TITL THE OLFACTOMEDIN DOMAIN FROM GLIOMEDIN IS A BETA-PROPELLER JRNL TITL 2 WITH UNIQUE STRUCTURAL PROPERTIES. JRNL REF J.BIOL.CHEM. V. 290 3612 2015 JRNL REFN ISSN 0021-9258 JRNL PMID 25525261 JRNL DOI 10.1074/JBC.M114.627547 REMARK 2 REMARK 2 RESOLUTION. 1.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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) : 1.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.08 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 78443 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.174 REMARK 3 R VALUE (WORKING SET) : 0.173 REMARK 3 FREE R VALUE : 0.212 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1565 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 43.1027 - 3.2244 0.99 7111 144 0.1559 0.1932 REMARK 3 2 3.2244 - 2.5594 1.00 7034 147 0.1624 0.1857 REMARK 3 3 2.5594 - 2.2359 1.00 7062 143 0.1523 0.2037 REMARK 3 4 2.2359 - 2.0314 0.99 7009 138 0.1483 0.1574 REMARK 3 5 2.0314 - 1.8858 0.99 6974 147 0.1587 0.2074 REMARK 3 6 1.8858 - 1.7746 0.99 6975 140 0.1731 0.2361 REMARK 3 7 1.7746 - 1.6858 0.99 7034 142 0.1987 0.2562 REMARK 3 8 1.6858 - 1.6124 0.99 6943 145 0.2122 0.2583 REMARK 3 9 1.6124 - 1.5503 0.98 6916 131 0.2347 0.2947 REMARK 3 10 1.5503 - 1.4968 0.98 6912 151 0.2680 0.3305 REMARK 3 11 1.4968 - 1.4500 0.97 6908 137 0.3065 0.3360 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) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.200 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.99 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 : 0.015 4208 REMARK 3 ANGLE : 1.029 5708 REMARK 3 CHIRALITY : 0.066 622 REMARK 3 PLANARITY : 0.006 724 REMARK 3 DIHEDRAL : 12.907 1533 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 4D7C COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 21-NOV-14. REMARK 100 THE DEPOSITION ID IS D_1290062361. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.873 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 78451 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.450 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.10000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 1.02000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.300 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: PDB ENTRY 4D77 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM SODIUM CITRATE PH 5.5, 20% PEG REMARK 280 3000 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 70.85000 REMARK 290 SMTRY3 2 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 259 REMARK 465 GLN A 260 REMARK 465 PRO A 261 REMARK 465 ASN A 262 REMARK 465 SER A 263 REMARK 465 PHE A 264 REMARK 465 THR A 265 REMARK 465 ASN A 266 REMARK 465 GLN A 267 REMARK 465 CYS A 268 REMARK 465 PRO A 269 REMARK 465 GLY A 270 REMARK 465 GLU A 271 REMARK 465 THR A 272 REMARK 465 CYS A 273 REMARK 465 VAL A 274 REMARK 465 ILE A 275 REMARK 465 PRO A 276 REMARK 465 ASN A 277 REMARK 465 ASP A 278 REMARK 465 ASP A 279 REMARK 465 THR A 280 REMARK 465 LEU A 281 REMARK 465 VAL A 282 REMARK 465 GLY A 283 REMARK 465 ARG A 284 REMARK 465 ALA A 285 REMARK 465 ASP A 286 REMARK 465 GLU A 287 REMARK 465 LYS A 288 REMARK 465 VAL A 289 REMARK 465 ASN A 290 REMARK 465 GLU A 291 REMARK 465 ARG A 292 REMARK 465 HIS A 293 REMARK 465 SER A 294 REMARK 465 PRO A 295 REMARK 465 GLN A 296 REMARK 465 THR A 297 REMARK 465 GLY B 259 REMARK 465 GLN B 260 REMARK 465 PRO B 261 REMARK 465 ASN B 262 REMARK 465 SER B 263 REMARK 465 PHE B 264 REMARK 465 THR B 265 REMARK 465 ASN B 266 REMARK 465 GLN B 267 REMARK 465 CYS B 268 REMARK 465 PRO B 269 REMARK 465 GLY B 270 REMARK 465 GLU B 271 REMARK 465 THR B 272 REMARK 465 CYS B 273 REMARK 465 VAL B 274 REMARK 465 ILE B 275 REMARK 465 PRO B 276 REMARK 465 ASN B 277 REMARK 465 ASP B 278 REMARK 465 ASP B 279 REMARK 465 THR B 280 REMARK 465 LEU B 281 REMARK 465 VAL B 282 REMARK 465 GLY B 283 REMARK 465 ARG B 284 REMARK 465 ALA B 285 REMARK 465 ASP B 286 REMARK 465 GLU B 287 REMARK 465 LYS B 288 REMARK 465 VAL B 289 REMARK 465 ASN B 290 REMARK 465 GLU B 291 REMARK 465 ARG B 292 REMARK 465 HIS B 293 REMARK 465 SER B 294 REMARK 465 PRO B 295 REMARK 465 GLN B 296 REMARK 465 THR B 297 REMARK 465 GLU B 298 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 2099 O HOH A 2104 2.06 REMARK 500 O HOH B 2104 O HOH B 2105 2.12 REMARK 500 O HOH B 2147 O HOH B 2207 2.12 REMARK 500 O HOH A 2183 O HOH B 2198 2.16 REMARK 500 O HOH A 2175 O HOH A 2176 2.17 REMARK 500 O HOH A 2008 O HOH A 2009 2.17 REMARK 500 ND2 ASN B 423 O HOH B 2152 2.18 REMARK 500 O HOH A 2113 O HOH B 2199 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 2233 O HOH B 2092 1554 2.10 REMARK 500 O HOH A 2086 O HOH A 2278 1556 2.16 REMARK 500 O HOH A 2248 O HOH B 2093 1554 2.18 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 ASN B 423 CB ASN B 423 CG 0.217 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 328 79.05 -66.27 REMARK 500 HIS A 337 -175.10 71.81 REMARK 500 ASN A 386 35.13 -98.63 REMARK 500 LYS A 395 -26.63 -151.48 REMARK 500 GLU A 396 84.60 56.21 REMARK 500 TYR A 408 -0.29 -151.52 REMARK 500 SER A 442 -51.50 -147.30 REMARK 500 HIS B 337 -169.01 68.93 REMARK 500 GLU B 396 130.04 -25.97 REMARK 500 THR B 397 -40.62 -143.26 REMARK 500 TYR B 408 3.54 -155.91 REMARK 500 SER B 442 -48.53 -146.94 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 GLU B 396 THR B 397 -147.26 REMARK 500 THR B 397 PRO B 398 -129.73 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 A2060 DISTANCE = 6.21 ANGSTROMS REMARK 525 HOH A2136 DISTANCE = 5.92 ANGSTROMS REMARK 525 HOH B2196 DISTANCE = 6.23 ANGSTROMS REMARK 525 HOH B2210 DISTANCE = 6.15 ANGSTROMS 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 NA A1544 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 423 OD1 REMARK 620 2 ASN A 471 OD1 110.0 REMARK 620 3 ALA A 472 O 98.1 88.3 REMARK 620 4 LEU A 517 O 131.3 118.2 89.6 REMARK 620 5 HOH A2188 O 92.1 91.3 169.3 81.2 REMARK 620 6 HOH A2189 O 73.7 170.8 82.8 59.6 97.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B1544 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN B 423 OD1 REMARK 620 2 ASN B 423 OD1 40.1 REMARK 620 3 ASN B 471 OD1 131.9 99.4 REMARK 620 4 ALA B 472 O 86.2 104.3 80.9 REMARK 620 5 LEU B 517 O 119.8 153.3 105.9 88.2 REMARK 620 6 HOH B2151 O 53.6 90.7 165.5 86.6 66.2 REMARK 620 7 HOH B2152 O 115.4 93.9 84.8 158.4 80.2 105.0 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 1544 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 1544 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4D77 RELATED DB: PDB REMARK 900 HIGH-RESOLUTION STRUCTURE OF THE EXTRACELLULAR OLFACTOMEDIN DOMAIN REMARK 900 FROM GLIOMEDIN DBREF 4D7C A 260 543 UNP Q80WL1 GLDN_RAT 260 543 DBREF 4D7C B 260 543 UNP Q80WL1 GLDN_RAT 260 543 SEQADV 4D7C GLY A 259 UNP Q80WL1 EXPRESSION TAG SEQADV 4D7C GLY B 259 UNP Q80WL1 EXPRESSION TAG SEQRES 1 A 285 GLY GLN PRO ASN SER PHE THR ASN GLN CYS PRO GLY GLU SEQRES 2 A 285 THR CYS VAL ILE PRO ASN ASP ASP THR LEU VAL GLY ARG SEQRES 3 A 285 ALA ASP GLU LYS VAL ASN GLU ARG HIS SER PRO GLN THR SEQRES 4 A 285 GLU PRO MET ILE THR SER ILE GLY ASN PRO ALA GLN VAL SEQRES 5 A 285 LEU LYS VAL LYS GLU THR PHE GLY THR TRP LEU ARG GLU SEQRES 6 A 285 SER ALA ASN ARG SER ASP ASP ARG ILE TRP VAL THR GLU SEQRES 7 A 285 HIS PHE SER GLY ILE MET VAL LYS GLU PHE GLU ASP LEU SEQRES 8 A 285 PRO ALA LEU LEU ASN SER SER PHE THR LEU LEU HIS LEU SEQRES 9 A 285 PRO HIS TYR PHE HIS GLY CYS GLY HIS ALA VAL TYR ASN SEQRES 10 A 285 ASN SER LEU TYR TYR HIS LYS GLY GLY SER ASN THR ILE SEQRES 11 A 285 VAL ARG PHE GLU PHE GLY LYS GLU THR PRO GLN THR LEU SEQRES 12 A 285 LYS LEU GLU ASP ALA LEU TYR PHE ASP ARG LYS TYR LEU SEQRES 13 A 285 PHE ALA ASN SER LYS THR TYR PHE ASN ILE ALA VAL ASP SEQRES 14 A 285 GLU LYS GLY LEU TRP ILE ILE TYR ALA SER SER VAL ASP SEQRES 15 A 285 GLY SER SER ILE LEU VAL ALA GLN LEU ASP GLU ARG THR SEQRES 16 A 285 PHE SER VAL LEU ARG HIS ILE ASN THR THR TYR PRO LYS SEQRES 17 A 285 SER LYS ALA GLY ASN ALA PHE ILE ALA GLN GLY ILE LEU SEQRES 18 A 285 TYR VAL THR ASP THR LYS ASP THR ARG VAL THR PHE ALA SEQRES 19 A 285 PHE ASP LEU LEU ARG GLY LYS GLN ILE ASN ALA ASN PHE SEQRES 20 A 285 GLY LEU ARG MET SER GLN SER VAL LEU ALA MET LEU SER SEQRES 21 A 285 TYR ASN MET ARG ASP GLN HIS LEU TYR SER TRP GLU ASP SEQRES 22 A 285 GLY HIS LEU MET LEU TYR PRO VAL HIS PHE SER SER SEQRES 1 B 285 GLY GLN PRO ASN SER PHE THR ASN GLN CYS PRO GLY GLU SEQRES 2 B 285 THR CYS VAL ILE PRO ASN ASP ASP THR LEU VAL GLY ARG SEQRES 3 B 285 ALA ASP GLU LYS VAL ASN GLU ARG HIS SER PRO GLN THR SEQRES 4 B 285 GLU PRO MET ILE THR SER ILE GLY ASN PRO ALA GLN VAL SEQRES 5 B 285 LEU LYS VAL LYS GLU THR PHE GLY THR TRP LEU ARG GLU SEQRES 6 B 285 SER ALA ASN ARG SER ASP ASP ARG ILE TRP VAL THR GLU SEQRES 7 B 285 HIS PHE SER GLY ILE MET VAL LYS GLU PHE GLU ASP LEU SEQRES 8 B 285 PRO ALA LEU LEU ASN SER SER PHE THR LEU LEU HIS LEU SEQRES 9 B 285 PRO HIS TYR PHE HIS GLY CYS GLY HIS ALA VAL TYR ASN SEQRES 10 B 285 ASN SER LEU TYR TYR HIS LYS GLY GLY SER ASN THR ILE SEQRES 11 B 285 VAL ARG PHE GLU PHE GLY LYS GLU THR PRO GLN THR LEU SEQRES 12 B 285 LYS LEU GLU ASP ALA LEU TYR PHE ASP ARG LYS TYR LEU SEQRES 13 B 285 PHE ALA ASN SER LYS THR TYR PHE ASN ILE ALA VAL ASP SEQRES 14 B 285 GLU LYS GLY LEU TRP ILE ILE TYR ALA SER SER VAL ASP SEQRES 15 B 285 GLY SER SER ILE LEU VAL ALA GLN LEU ASP GLU ARG THR SEQRES 16 B 285 PHE SER VAL LEU ARG HIS ILE ASN THR THR TYR PRO LYS SEQRES 17 B 285 SER LYS ALA GLY ASN ALA PHE ILE ALA GLN GLY ILE LEU SEQRES 18 B 285 TYR VAL THR ASP THR LYS ASP THR ARG VAL THR PHE ALA SEQRES 19 B 285 PHE ASP LEU LEU ARG GLY LYS GLN ILE ASN ALA ASN PHE SEQRES 20 B 285 GLY LEU ARG MET SER GLN SER VAL LEU ALA MET LEU SER SEQRES 21 B 285 TYR ASN MET ARG ASP GLN HIS LEU TYR SER TRP GLU ASP SEQRES 22 B 285 GLY HIS LEU MET LEU TYR PRO VAL HIS PHE SER SER HET NA A1544 1 HET NA B1544 1 HETNAM NA SODIUM ION FORMUL 3 NA 2(NA 1+) FORMUL 5 HOH *561(H2 O) HELIX 1 1 ASP A 348 ASN A 354 1 7 HELIX 2 2 ALA A 416 LYS A 419 5 4 HELIX 3 3 SER A 467 ALA A 469 5 3 HELIX 4 4 ASP B 348 ASN B 354 1 7 HELIX 5 5 ALA B 416 LYS B 419 5 4 HELIX 6 6 SER B 467 ALA B 469 5 3 SHEET 1 AA 2 ILE A 301 ILE A 304 0 SHEET 2 AA 2 HIS A 533 PHE A 541 -1 O HIS A 540 N THR A 302 SHEET 1 AB 2 ALA A 308 LYS A 312 0 SHEET 2 AB 2 HIS A 533 PHE A 541 -1 O LEU A 534 N VAL A 310 SHEET 1 AC 4 LEU A 514 ASN A 520 0 SHEET 2 AC 4 HIS A 525 GLU A 530 -1 O HIS A 525 N ASN A 520 SHEET 3 AC 4 HIS A 533 PHE A 541 -1 O HIS A 533 N GLU A 530 SHEET 4 AC 4 ALA A 308 LYS A 312 -1 O ALA A 308 N LEU A 536 SHEET 1 AD 4 LEU A 514 ASN A 520 0 SHEET 2 AD 4 HIS A 525 GLU A 530 -1 O HIS A 525 N ASN A 520 SHEET 3 AD 4 HIS A 533 PHE A 541 -1 O HIS A 533 N GLU A 530 SHEET 4 AD 4 ILE A 301 ILE A 304 -1 N THR A 302 O HIS A 540 SHEET 1 AE 4 GLY A 318 ARG A 322 0 SHEET 2 AE 4 ILE A 332 GLU A 336 -1 O TRP A 333 N LEU A 321 SHEET 3 AE 4 SER A 339 PHE A 346 -1 O LYS A 344 N VAL A 334 SHEET 4 AE 4 THR A 358 HIS A 367 -1 O THR A 358 N GLU A 345 SHEET 1 AF 4 ALA A 372 VAL A 373 0 SHEET 2 AF 4 SER A 377 HIS A 381 -1 O TYR A 379 N ALA A 372 SHEET 3 AF 4 THR A 387 GLU A 392 -1 O VAL A 389 N TYR A 380 SHEET 4 AF 4 GLN A 399 LYS A 402 -1 O GLN A 399 N ARG A 390 SHEET 1 AG 4 ASN A 423 ASP A 427 0 SHEET 2 AG 4 GLY A 430 ALA A 436 -1 O GLY A 430 N ASP A 427 SHEET 3 AG 4 SER A 443 ASP A 450 -1 O LEU A 445 N TYR A 435 SHEET 4 AG 4 SER A 455 PRO A 465 -1 O SER A 455 N ASP A 450 SHEET 1 AH 4 ALA A 472 ALA A 475 0 SHEET 2 AH 4 ILE A 478 THR A 482 -1 O ILE A 478 N ALA A 475 SHEET 3 AH 4 ARG A 488 ASP A 494 -1 N THR A 490 O VAL A 481 SHEET 4 AH 4 LYS A 499 ILE A 501 1 O LYS A 499 N ASP A 494 SHEET 1 AI 4 ALA A 472 ALA A 475 0 SHEET 2 AI 4 ILE A 478 THR A 482 -1 O ILE A 478 N ALA A 475 SHEET 3 AI 4 ARG A 488 ASP A 494 -1 N THR A 490 O VAL A 481 SHEET 4 AI 4 PHE A 505 GLY A 506 -1 O PHE A 505 N VAL A 489 SHEET 1 AJ 2 LYS A 499 ILE A 501 0 SHEET 2 AJ 2 ARG A 488 ASP A 494 1 O ALA A 492 N ILE A 501 SHEET 1 BA 2 ILE B 301 ILE B 304 0 SHEET 2 BA 2 HIS B 533 PHE B 541 -1 O HIS B 540 N THR B 302 SHEET 1 BB 2 ALA B 308 LYS B 312 0 SHEET 2 BB 2 HIS B 533 PHE B 541 -1 O LEU B 534 N VAL B 310 SHEET 1 BC 4 LEU B 514 ASN B 520 0 SHEET 2 BC 4 HIS B 525 GLU B 530 -1 O HIS B 525 N ASN B 520 SHEET 3 BC 4 HIS B 533 PHE B 541 -1 O HIS B 533 N GLU B 530 SHEET 4 BC 4 ALA B 308 LYS B 312 -1 O ALA B 308 N LEU B 536 SHEET 1 BD 4 LEU B 514 ASN B 520 0 SHEET 2 BD 4 HIS B 525 GLU B 530 -1 O HIS B 525 N ASN B 520 SHEET 3 BD 4 HIS B 533 PHE B 541 -1 O HIS B 533 N GLU B 530 SHEET 4 BD 4 ILE B 301 ILE B 304 -1 N THR B 302 O HIS B 540 SHEET 1 BE 7 GLY B 318 ARG B 322 0 SHEET 2 BE 7 ILE B 332 GLU B 336 -1 O TRP B 333 N LEU B 321 SHEET 3 BE 7 SER B 339 PHE B 346 -1 O LYS B 344 N VAL B 334 SHEET 4 BE 7 THR B 358 VAL B 373 -1 O THR B 358 N GLU B 345 SHEET 5 BE 7 SER B 377 LYS B 382 -1 O TYR B 379 N ALA B 372 SHEET 6 BE 7 THR B 387 GLU B 392 -1 O THR B 387 N LYS B 382 SHEET 7 BE 7 GLN B 399 LYS B 402 -1 O GLN B 399 N ARG B 390 SHEET 1 BF 4 ASN B 423 ASP B 427 0 SHEET 2 BF 4 GLY B 430 ALA B 436 -1 O GLY B 430 N ASP B 427 SHEET 3 BF 4 SER B 443 ASP B 450 -1 O LEU B 445 N TYR B 435 SHEET 4 BF 4 SER B 455 PRO B 465 -1 O SER B 455 N ASP B 450 SHEET 1 BG 4 ALA B 472 ALA B 475 0 SHEET 2 BG 4 ILE B 478 THR B 482 -1 O ILE B 478 N ALA B 475 SHEET 3 BG 4 ARG B 488 ASP B 494 -1 N THR B 490 O VAL B 481 SHEET 4 BG 4 LYS B 499 ILE B 501 1 O LYS B 499 N ASP B 494 SHEET 1 BH 4 ALA B 472 ALA B 475 0 SHEET 2 BH 4 ILE B 478 THR B 482 -1 O ILE B 478 N ALA B 475 SHEET 3 BH 4 ARG B 488 ASP B 494 -1 N THR B 490 O VAL B 481 SHEET 4 BH 4 PHE B 505 GLY B 506 -1 O PHE B 505 N VAL B 489 SHEET 1 BI 2 LYS B 499 ILE B 501 0 SHEET 2 BI 2 ARG B 488 ASP B 494 1 O ALA B 492 N ILE B 501 LINK OD1 ASN A 423 NA NA A1544 1555 1555 2.33 LINK OD1 ASN A 471 NA NA A1544 1555 1555 2.39 LINK O ALA A 472 NA NA A1544 1555 1555 2.30 LINK O LEU A 517 NA NA A1544 1555 1555 2.32 LINK NA NA A1544 O HOH A2188 1555 1555 2.46 LINK NA NA A1544 O HOH A2189 1555 1555 2.95 LINK OD1AASN B 423 NA NA B1544 1555 1555 2.25 LINK OD1BASN B 423 NA NA B1544 1555 1555 1.91 LINK OD1 ASN B 471 NA NA B1544 1555 1555 2.64 LINK O ALA B 472 NA NA B1544 1555 1555 2.31 LINK O LEU B 517 NA NA B1544 1555 1555 2.39 LINK NA NA B1544 O HOH B2151 1555 1555 2.81 LINK NA NA B1544 O HOH B2152 1555 1555 2.51 SITE 1 AC1 6 ASN B 423 ASN B 471 ALA B 472 LEU B 517 SITE 2 AC1 6 HOH B2151 HOH B2152 SITE 1 AC2 6 ASN A 423 ASN A 471 ALA A 472 LEU A 517 SITE 2 AC2 6 HOH A2188 HOH A2189 CRYST1 37.550 141.700 46.030 90.00 110.61 90.00 P 1 21 1 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 0.026631 0.000000 0.010015 0.00000 SCALE2 0.000000 0.007057 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023210 0.00000