HEADER RECEPTOR 29-OCT-01 1GP3 TITLE HUMAN IGF2R DOMAIN 11 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CATION-INDEPENDENT MANNOSE-6-PHOSPHATE RECEPTOR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: IGF-II BINDING DOMAIN REPEAT 11 RESIDUES 1508-1650; COMPND 5 SYNONYM: INSULIN-LIKE GROWTH FACTOR II RECEPTOR, CI MAN-6-P, COMPND 6 RECEPTOR, CI-MPR, 300 KDA MANNOSE 6-PHOSPHATE RECEPTOR, MPR 300, COMPND 7 MPR300; COMPND 8 ENGINEERED: YES; COMPND 9 OTHER_DETAILS: RESIDUES VISIBLE IN THE ELECTRON DENSITY MAP COMPND 10 CORRESPOND TO MATURE IGF2R RESIDUE NUMBERS 1515 -1647, WITH THE COMPND 11 EXCEPTION OF RESIDUES 1618 - 1621 WHERE THE DENSITY IS NOT CONTINUOUS SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 ATCC: 95661; SOURCE 6 TISSUE: PLACENTA; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_VARIANT: ORIGAMI; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET22B KEYWDS RECEPTOR, INSULIN-LIKE GROWTH FACTOR, CATION INDEPENDENT MANNOSE 6- KEYWDS 2 PHOSPHATE, TRANSPORT, BETA BARREL EXPDTA X-RAY DIFFRACTION AUTHOR J.BROWN,R.M.ESNOUF,M.A.JONES,J.LINNELL,K.HARLOS,A.B.HASSAN,E.Y.JONES REVDAT 4 13-DEC-23 1GP3 1 REMARK REVDAT 3 10-APR-19 1GP3 1 SOURCE REVDAT 2 24-FEB-09 1GP3 1 VERSN REVDAT 1 28-FEB-02 1GP3 0 JRNL AUTH J.BROWN,R.M.ESNOUF,M.A.JONES,J.LINNELL,K.HARLOS,A.B.HASSAN, JRNL AUTH 2 E.Y.JONES JRNL TITL STRUCTURE OF A FUNCTIONAL IGF2R FRAGMENT DETERMINED FROM THE JRNL TITL 2 ANOMALOUS SCATTERING OF SULFUR JRNL REF EMBO J. V. 21 1054 2002 JRNL REFN ISSN 0261-4189 JRNL PMID 11867533 JRNL DOI 10.1093/EMBOJ/21.5.1054 REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.35 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 397551.980 REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 94.1 REMARK 3 NUMBER OF REFLECTIONS : 9427 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.206 REMARK 3 FREE R VALUE : 0.255 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 492 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.012 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.95 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.07 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 84.90 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1313 REMARK 3 BIN R VALUE (WORKING SET) : 0.2320 REMARK 3 BIN FREE R VALUE : 0.3030 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.90 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 68 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.037 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 983 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 78 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.75000 REMARK 3 B22 (A**2) : -2.17000 REMARK 3 B33 (A**2) : 3.92000 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.23 REMARK 3 ESD FROM SIGMAA (A) : 0.15 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.33 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.23 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 26.10 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.720 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.630 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.700 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.580 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.900 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.36 REMARK 3 BSOL : 41.41 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1GP3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 29-OCT-01. REMARK 100 THE DEPOSITION ID IS D_1290008776. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-SEP-00 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 8.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.934 REMARK 200 MONOCHROMATOR : DIAMOND (111), GE(220) REMARK 200 OPTICS : TOROIDAL MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9752 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 200 DATA REDUNDANCY : 7.700 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.02 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.65300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: EPMR REMARK 200 STARTING MODEL: 1GP0 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.95 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN WAS CRYSTALLIZED FROM 0.2 M REMARK 280 SODIUM ACETATE, 0.1 M TRIS HCL PH 8.5, 30 % W/V PEG 4000, PH 8.50 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 15.68650 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 41.51500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.92150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 41.51500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 15.68650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 24.92150 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS 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 400 REMARK 400 COMPOUND REMARK 400 TRANSPORT OF PHOSPHORYLATED LYSOSOMAL ENZYMES FROM REMARK 400 THE GOLGI COMPLEX AND THE CELL SURFACE TO LYSOSOMES. LYSOSOMAL REMARK 400 ENZYMES BEARING PHOSPHOMANNOSYL RESIDUES BIND SPECIFICALLY TO REMARK 400 MANNOSE-6-PHOSPHATE RECEPTORS IN THE GOLGI APPARATUS AND THE REMARK 400 RESULTING RECEPTOR-LIGAND COMPLEX IS TRANSPORTED TO AN ACIDIC REMARK 400 PRELYOSOMAL COMPARTMENT WHERE THE LOW PH MEDIATES THE DISSOCIATION REMARK 400 OF THE COMPLEX. THIS RECEPTOR ALSO BINDS INSULIN GROWTH FACTOR II. 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 1508 REMARK 465 LYS A 1509 REMARK 465 SER A 1510 REMARK 465 ASN A 1511 REMARK 465 GLU A 1512 REMARK 465 HIS A 1513 REMARK 465 ASP A 1514 REMARK 465 ALA A 1618 REMARK 465 GLY A 1619 REMARK 465 PRO A 1620 REMARK 465 THR A 1621 REMARK 465 GLN A 1648 REMARK 465 ALA A 1649 REMARK 465 THR A 1650 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 CYS A1516 80.90 -158.63 REMARK 500 SER A1543 -156.96 58.50 REMARK 500 GLN A1586 -0.53 73.34 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1E6F RELATED DB: PDB REMARK 900 HUMAN MIR-RECEPTOR, REPEAT 11 REMARK 900 RELATED ID: 1GP0 RELATED DB: PDB REMARK 900 STRUCTURE OF A FUNCTIONAL IGF2R FRAGMENT DETERMINED FROM ANOMALOUS REMARK 900 SCATTERING OF SULPHUR DBREF 1GP3 A 1508 1650 UNP P11717 MPRI_HUMAN 1508 1650 SEQRES 1 A 143 MET LYS SER ASN GLU HIS ASP ASP CYS GLN VAL THR ASN SEQRES 2 A 143 PRO SER THR GLY HIS LEU PHE ASP LEU SER SER LEU SER SEQRES 3 A 143 GLY ARG ALA GLY PHE THR ALA ALA TYR SER GLU LYS GLY SEQRES 4 A 143 LEU VAL TYR MET SER ILE CYS GLY GLU ASN GLU ASN CYS SEQRES 5 A 143 PRO PRO GLY VAL GLY ALA CYS PHE GLY GLN THR ARG ILE SEQRES 6 A 143 SER VAL GLY LYS ALA ASN LYS ARG LEU ARG TYR VAL ASP SEQRES 7 A 143 GLN VAL LEU GLN LEU VAL TYR LYS ASP GLY SER PRO CYS SEQRES 8 A 143 PRO SER LYS SER GLY LEU SER TYR LYS SER VAL ILE SER SEQRES 9 A 143 PHE VAL CYS ARG PRO GLU ALA GLY PRO THR ASN ARG PRO SEQRES 10 A 143 MET LEU ILE SER LEU ASP LYS GLN THR CYS THR LEU PHE SEQRES 11 A 143 PHE SER TRP HIS THR PRO LEU ALA CYS GLU GLN ALA THR FORMUL 2 HOH *78(H2 O) HELIX 1 1 SER A 1530 SER A 1533 5 4 HELIX 2 2 PRO A 1643 CYS A 1646 5 4 SHEET 1 AA 2 GLN A1517 THR A1519 0 SHEET 2 AA 2 LEU A1526 ASP A1528 -1 O PHE A1527 N VAL A1518 SHEET 1 AB 3 PHE A1538 TYR A1542 0 SHEET 2 AB 3 GLY A1546 MET A1550 -1 O GLY A1546 N TYR A1542 SHEET 3 AB 3 ALA A1565 PHE A1567 -1 O CYS A1566 N TYR A1549 SHEET 1 AC 5 ARG A1582 VAL A1584 0 SHEET 2 AC 5 VAL A1587 TYR A1592 -1 O VAL A1587 N VAL A1584 SHEET 3 AC 5 LYS A1607 CYS A1614 -1 O SER A1608 N TYR A1592 SHEET 4 AC 5 THR A1635 THR A1642 1 O LEU A1636 N VAL A1609 SHEET 5 AC 5 MET A1625 ASP A1630 -1 O MET A1625 N SER A1639 SSBOND 1 CYS A 1516 CYS A 1553 1555 1555 2.03 SSBOND 2 CYS A 1559 CYS A 1566 1555 1555 2.04 SSBOND 3 CYS A 1598 CYS A 1634 1555 1555 2.03 SSBOND 4 CYS A 1614 CYS A 1646 1555 1555 2.03 CRYST1 31.373 49.843 83.030 90.00 90.00 90.00 P 21 21 21 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 0.031874 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020063 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012044 0.00000