HEADER TRANSFERASE 02-JUL-12 4FWW TITLE CRYSTAL STRUCTURE OF THE SEMA-PSI EXTRACELLULAR DOMAINS OF HUMAN RON TITLE 2 RECEPTOR TYROSINE KINASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: MACROPHAGE-STIMULATING PROTEIN RECEPTOR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: EXTRACELLULAR SEMA AND PSI DOMAINS (UNP RESIDUES 42-568); COMPND 5 SYNONYM: MSP RECEPTOR, CDW136, PROTEIN-TYROSINE KINASE 8, P185-RON, COMPND 6 MACROPHAGE-STIMULATING PROTEIN RECEPTOR ALPHA CHAIN, MACROPHAGE- COMPND 7 STIMULATING PROTEIN RECEPTOR BETA CHAIN; COMPND 8 EC: 2.7.10.1; COMPND 9 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: MST1R, PTK8, RON; SOURCE 6 EXPRESSION_SYSTEM: DROSOPHILA MELANOGASTER; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7227; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: SCHNEIDER 2; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PMT/BIP-V5-HISA KEYWDS BETA-PROPELLER, CYSTEINE-KNOT, RECEPTOR TYROSINE KINASE, MACROPHAGE KEYWDS 2 STIMULATING PROTEIN, N-GLYCOSYLATION, EXTRACELLULAR, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR K.L.CHAO,O.HERZBERG REVDAT 5 13-SEP-23 4FWW 1 REMARK HETSYN REVDAT 4 29-JUL-20 4FWW 1 COMPND REMARK SEQADV HETNAM REVDAT 4 2 1 LINK SITE ATOM REVDAT 3 15-NOV-17 4FWW 1 REMARK REVDAT 2 22-AUG-12 4FWW 1 JRNL REVDAT 1 08-AUG-12 4FWW 0 JRNL AUTH K.L.CHAO,I.W.TSAI,C.CHEN,O.HERZBERG JRNL TITL CRYSTAL STRUCTURE OF THE SEMA-PSI EXTRACELLULAR DOMAIN OF JRNL TITL 2 HUMAN RON RECEPTOR TYROSINE KINASE. JRNL REF PLOS ONE V. 7 41912 2012 JRNL REFN ESSN 1932-6203 JRNL PMID 22848655 JRNL DOI 10.1371/JOURNAL.PONE.0041912 REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.32 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 90.0 REMARK 3 NUMBER OF REFLECTIONS : 48882 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 + TEST SET) : 0.193 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.232 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2627 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.85 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.90 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2504 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 63.56 REMARK 3 BIN R VALUE (WORKING SET) : 0.3620 REMARK 3 BIN FREE R VALUE SET COUNT : 133 REMARK 3 BIN FREE R VALUE : 0.4320 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3845 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 127 REMARK 3 SOLVENT ATOMS : 358 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 51.63 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.01000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : -0.01000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.01000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.137 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.134 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.110 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.857 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.962 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.943 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4031 ; 0.012 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5497 ; 1.548 ; 1.990 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 510 ; 8.048 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 160 ;34.483 ;23.688 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 548 ;15.249 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 21 ;20.998 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 627 ; 0.125 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3080 ; 0.013 ; 0.022 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1829 ; 0.231 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2733 ; 0.315 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 340 ; 0.192 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 70 ; 0.211 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 18 ; 0.307 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2657 ; 1.032 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4174 ; 1.690 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1600 ; 2.720 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1430 ; 4.159 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 42 A 266 REMARK 3 ORIGIN FOR THE GROUP (A): 10.3190 -12.3320 24.5300 REMARK 3 T TENSOR REMARK 3 T11: 0.0794 T22: 0.1137 REMARK 3 T33: 0.1143 T12: -0.0073 REMARK 3 T13: 0.0137 T23: -0.0686 REMARK 3 L TENSOR REMARK 3 L11: 2.2536 L22: 1.2007 REMARK 3 L33: 1.6772 L12: 0.8368 REMARK 3 L13: -0.1810 L23: -0.4306 REMARK 3 S TENSOR REMARK 3 S11: -0.1237 S12: 0.1117 S13: -0.2665 REMARK 3 S21: -0.1763 S22: 0.1255 S23: -0.3191 REMARK 3 S31: 0.0862 S32: 0.3130 S33: -0.0018 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 267 A 391 REMARK 3 ORIGIN FOR THE GROUP (A): -14.8220 -6.6060 23.5060 REMARK 3 T TENSOR REMARK 3 T11: 0.0299 T22: 0.1020 REMARK 3 T33: 0.0771 T12: -0.0089 REMARK 3 T13: -0.0281 T23: -0.0083 REMARK 3 L TENSOR REMARK 3 L11: 1.6739 L22: 2.9013 REMARK 3 L33: 3.4434 L12: 0.3156 REMARK 3 L13: -0.3753 L23: -1.9903 REMARK 3 S TENSOR REMARK 3 S11: -0.0354 S12: 0.2745 S13: 0.0011 REMARK 3 S21: -0.2530 S22: 0.1982 S23: 0.2764 REMARK 3 S31: 0.0666 S32: -0.4128 S33: -0.1629 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 392 A 522 REMARK 3 ORIGIN FOR THE GROUP (A): -8.2190 -2.7110 19.8850 REMARK 3 T TENSOR REMARK 3 T11: 0.0562 T22: 0.1224 REMARK 3 T33: 0.0609 T12: -0.0146 REMARK 3 T13: -0.0230 T23: -0.0072 REMARK 3 L TENSOR REMARK 3 L11: 1.2733 L22: 2.3730 REMARK 3 L33: 1.9481 L12: 0.9331 REMARK 3 L13: -0.6072 L23: -1.1763 REMARK 3 S TENSOR REMARK 3 S11: 0.0312 S12: 0.2260 S13: 0.1286 REMARK 3 S21: 0.0254 S22: 0.1020 S23: 0.1927 REMARK 3 S31: -0.1702 S32: -0.0291 S33: -0.1332 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 523 A 568 REMARK 3 ORIGIN FOR THE GROUP (A): -1.4820 30.2000 15.8560 REMARK 3 T TENSOR REMARK 3 T11: 0.5032 T22: 0.1670 REMARK 3 T33: 0.3795 T12: -0.0759 REMARK 3 T13: 0.0760 T23: -0.0567 REMARK 3 L TENSOR REMARK 3 L11: 1.9577 L22: 22.0179 REMARK 3 L33: 4.7498 L12: -1.5380 REMARK 3 L13: 0.1438 L23: 1.8362 REMARK 3 S TENSOR REMARK 3 S11: -0.0956 S12: 0.2675 S13: -0.3962 REMARK 3 S21: -0.6213 S22: -0.0502 S23: -0.0807 REMARK 3 S31: 0.4087 S32: 0.0894 S33: 0.1459 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN USED IF PRESENT IN REMARK 3 THE INPUT REMARK 4 REMARK 4 4FWW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-JUL-12. REMARK 100 THE DEPOSITION ID IS D_1000073457. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-FEB-10 REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 23-ID-B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0332 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 51510 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 19.320 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.0 REMARK 200 DATA REDUNDANCY : 2.800 REMARK 200 R MERGE (I) : 0.06900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.4600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 63.7 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : 0.44000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.470 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 2UZX CHAIN B REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.38 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 19% PEG 4000, 0.1 M SODIUM ACETATE, PH REMARK 280 4.6, 0.2 M AMMONIUM SULFATE, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 53.20000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.65000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 53.20000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 36.65000 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: PISA 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 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 LYS A 305 REMARK 465 LEU A 306 REMARK 465 VAL A 307 REMARK 465 PRO A 308 REMARK 465 ARG A 309 REMARK 465 GLY A 310 REMARK 465 SER A 311 REMARK 465 PRO A 312 REMARK 465 GLU A 313 REMARK 465 GLY A 314 REMARK 465 ASP A 355 REMARK 465 GLY A 356 REMARK 465 GLY A 357 REMARK 465 PRO A 358 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 VAL A 42 CG1 CG2 REMARK 480 LYS A 43 CD CE NZ REMARK 480 ARG A 65 CG CD NE CZ NH1 NH2 REMARK 480 ALA A 166 CB REMARK 480 ARG A 170 CG CD NE CZ NH1 NH2 REMARK 480 ARG A 528 CD NE CZ NH1 NH2 REMARK 480 ARG A 535 CG CD NE CZ NH1 NH2 REMARK 480 ARG A 538 CB CG CD NE CZ NH1 NH2 REMARK 480 LYS A 556 CG CD CE NZ 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 NH1 ARG A 384 OG SER A 430 2.09 REMARK 500 OE1 GLU A 383 OE1 GLU A 387 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 O1 GOL A 613 O HOH A 1238 2556 2.00 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 VAL A 42 CB VAL A 42 CG2 -0.154 REMARK 500 HIS A 463 CG HIS A 463 CD2 0.060 REMARK 500 ARG A 535 CB ARG A 535 CG -0.515 REMARK 500 ARG A 538 CA ARG A 538 CB -0.248 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 VAL A 42 CA - CB - CG2 ANGL. DEV. = 12.1 DEGREES REMARK 500 ARG A 528 CB - CG - CD ANGL. DEV. = 26.8 DEGREES REMARK 500 ARG A 528 CG - CD - NE ANGL. DEV. = -15.7 DEGREES REMARK 500 ARG A 535 CA - CB - CG ANGL. DEV. = 17.9 DEGREES REMARK 500 ARG A 538 CB - CA - C ANGL. DEV. = 18.8 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 ASN A 76 -0.17 62.55 REMARK 500 GLN A 151 77.33 -151.52 REMARK 500 ALA A 154 -166.25 -107.71 REMARK 500 HIS A 168 -11.82 178.36 REMARK 500 ASP A 173 101.74 -162.66 REMARK 500 ARG A 214 173.16 67.05 REMARK 500 ASP A 272 122.00 -31.19 REMARK 500 ASP A 292 38.79 -97.39 REMARK 500 SER A 388 -116.32 83.42 REMARK 500 ASP A 437 112.43 -37.40 REMARK 500 ASP A 457 -114.29 51.67 REMARK 500 SER A 487 147.54 -171.33 REMARK 500 ASP A 493 28.17 -148.31 REMARK 500 HIS A 541 -66.01 -9.79 REMARK 500 MET A 551 141.45 177.75 REMARK 500 CYS A 558 64.12 -161.81 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 A 387 SER A 388 144.04 REMARK 500 SER A 388 PRO A 389 149.85 REMARK 500 REMARK 500 REMARK: NULL DBREF 4FWW A 42 568 UNP Q04912 RON_HUMAN 42 568 SEQADV 4FWW LEU A 306 UNP Q04912 ARG 306 CONFLICT SEQADV 4FWW VAL A 307 UNP Q04912 ARG 307 CONFLICT SEQADV 4FWW PRO A 308 UNP Q04912 ARG 308 CONFLICT SEQADV 4FWW SER A 311 UNP Q04912 ALA 311 CONFLICT SEQADV 4FWW GLN A 322 UNP Q04912 ARG 322 CONFLICT SEQRES 1 A 527 VAL LYS TYR VAL VAL PRO SER PHE SER ALA GLY GLY LEU SEQRES 2 A 527 VAL GLN ALA MET VAL THR TYR GLU GLY ASP ARG ASN GLU SEQRES 3 A 527 SER ALA VAL PHE VAL ALA ILE ARG ASN ARG LEU HIS VAL SEQRES 4 A 527 LEU GLY PRO ASP LEU LYS SER VAL GLN SER LEU ALA THR SEQRES 5 A 527 GLY PRO ALA GLY ASP PRO GLY CYS GLN THR CYS ALA ALA SEQRES 6 A 527 CYS GLY PRO GLY PRO HIS GLY PRO PRO GLY ASP THR ASP SEQRES 7 A 527 THR LYS VAL LEU VAL LEU ASP PRO ALA LEU PRO ALA LEU SEQRES 8 A 527 VAL SER CYS GLY SER SER LEU GLN GLY ARG CYS PHE LEU SEQRES 9 A 527 HIS ASP LEU GLU PRO GLN GLY THR ALA VAL HIS LEU ALA SEQRES 10 A 527 ALA PRO ALA CYS LEU PHE SER ALA HIS HIS ASN ARG PRO SEQRES 11 A 527 ASP ASP CYS PRO ASP CYS VAL ALA SER PRO LEU GLY THR SEQRES 12 A 527 ARG VAL THR VAL VAL GLU GLN GLY GLN ALA SER TYR PHE SEQRES 13 A 527 TYR VAL ALA SER SER LEU ASP ALA ALA VAL ALA ALA SER SEQRES 14 A 527 PHE SER PRO ARG SER VAL SER ILE ARG ARG LEU LYS ALA SEQRES 15 A 527 ASP ALA SER GLY PHE ALA PRO GLY PHE VAL ALA LEU SER SEQRES 16 A 527 VAL LEU PRO LYS HIS LEU VAL SER TYR SER ILE GLU TYR SEQRES 17 A 527 VAL HIS SER PHE HIS THR GLY ALA PHE VAL TYR PHE LEU SEQRES 18 A 527 THR VAL GLN PRO ALA SER VAL THR ASP ASP PRO SER ALA SEQRES 19 A 527 LEU HIS THR ARG LEU ALA ARG LEU SER ALA THR GLU PRO SEQRES 20 A 527 GLU LEU GLY ASP TYR ARG GLU LEU VAL LEU ASP CYS ARG SEQRES 21 A 527 PHE ALA PRO LYS LEU VAL PRO ARG GLY SER PRO GLU GLY SEQRES 22 A 527 GLY GLN PRO TYR PRO VAL LEU GLN VAL ALA HIS SER ALA SEQRES 23 A 527 PRO VAL GLY ALA GLN LEU ALA THR GLU LEU SER ILE ALA SEQRES 24 A 527 GLU GLY GLN GLU VAL LEU PHE GLY VAL PHE VAL THR GLY SEQRES 25 A 527 LYS ASP GLY GLY PRO GLY VAL GLY PRO ASN SER VAL VAL SEQRES 26 A 527 CYS ALA PHE PRO ILE ASP LEU LEU ASP THR LEU ILE ASP SEQRES 27 A 527 GLU GLY VAL GLU ARG CYS CYS GLU SER PRO VAL HIS PRO SEQRES 28 A 527 GLY LEU ARG ARG GLY LEU ASP PHE PHE GLN SER PRO SER SEQRES 29 A 527 PHE CYS PRO ASN PRO PRO GLY LEU GLU ALA LEU SER PRO SEQRES 30 A 527 ASN THR SER CYS ARG HIS PHE PRO LEU LEU VAL SER SER SEQRES 31 A 527 SER PHE SER ARG VAL ASP LEU PHE ASN GLY LEU LEU GLY SEQRES 32 A 527 PRO VAL GLN VAL THR ALA LEU TYR VAL THR ARG LEU ASP SEQRES 33 A 527 ASN VAL THR VAL ALA HIS MET GLY THR MET ASP GLY ARG SEQRES 34 A 527 ILE LEU GLN VAL GLU LEU VAL ARG SER LEU ASN TYR LEU SEQRES 35 A 527 LEU TYR VAL SER ASN PHE SER LEU GLY ASP SER GLY GLN SEQRES 36 A 527 PRO VAL GLN ARG ASP VAL SER ARG LEU GLY ASP HIS LEU SEQRES 37 A 527 LEU PHE ALA SER GLY ASP GLN VAL PHE GLN VAL PRO ILE SEQRES 38 A 527 GLN GLY PRO GLY CYS ARG HIS PHE LEU THR CYS GLY ARG SEQRES 39 A 527 CYS LEU ARG ALA TRP HIS PHE MET GLY CYS GLY TRP CYS SEQRES 40 A 527 GLY ASN MET CYS GLY GLN GLN LYS GLU CYS PRO GLY SER SEQRES 41 A 527 TRP GLN GLN ASP HIS CYS PRO MODRES 4FWW ASN A 488 ASN GLYCOSYLATION SITE HET NAG B 1 14 HET NAG B 2 14 HET BMA B 3 11 HET BMA B 4 11 HET SO4 A 605 5 HET SO4 A 606 5 HET ACT A 607 4 HET ACT A 608 4 HET ACT A 609 4 HET ACT A 610 4 HET ACT A 611 4 HET GOL A 612 6 HET GOL A 613 6 HET GOL A 614 6 HET GOL A 615 6 HET EDO A 616 4 HET EDO A 617 4 HET EDO A 618 4 HET EDO A 619 4 HET PEG A 620 7 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM BMA BETA-D-MANNOPYRANOSE HETNAM SO4 SULFATE ION HETNAM ACT ACETATE ION HETNAM GOL GLYCEROL HETNAM EDO 1,2-ETHANEDIOL HETNAM PEG DI(HYDROXYETHYL)ETHER HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE HETSYN BMA BETA-D-MANNOSE; D-MANNOSE; MANNOSE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 NAG 2(C8 H15 N O6) FORMUL 2 BMA 2(C6 H12 O6) FORMUL 3 SO4 2(O4 S 2-) FORMUL 5 ACT 5(C2 H3 O2 1-) FORMUL 10 GOL 4(C3 H8 O3) FORMUL 14 EDO 4(C2 H6 O2) FORMUL 18 PEG C4 H10 O3 FORMUL 19 HOH *358(H2 O) HELIX 1 1 CYS A 101 ALA A 106 1 6 HELIX 2 2 SER A 138 GLY A 141 5 4 HELIX 3 3 ASP A 204 ALA A 209 1 6 HELIX 4 4 LEU A 238 VAL A 243 1 6 HELIX 5 5 GLY A 330 SER A 338 1 9 HELIX 6 6 ILE A 371 GLU A 387 1 17 HELIX 7 7 SER A 421 PHE A 425 5 5 HELIX 8 8 GLY A 526 PHE A 530 5 5 HELIX 9 9 THR A 532 ALA A 539 1 8 HELIX 10 10 TRP A 540 GLY A 544 5 5 HELIX 11 11 GLN A 554 CYS A 558 5 5 SHEET 1 A 5 LYS A 43 VAL A 45 0 SHEET 2 A 5 TYR A 485 LEU A 491 1 O SER A 490 N LYS A 43 SHEET 3 A 5 ARG A 470 GLU A 475 -1 N GLN A 473 O VAL A 486 SHEET 4 A 5 VAL A 459 THR A 466 -1 N MET A 464 O LEU A 472 SHEET 5 A 5 VAL A 448 LEU A 456 -1 N TYR A 452 O HIS A 463 SHEET 1 B 4 PHE A 49 SER A 50 0 SHEET 2 B 4 GLN A 516 PRO A 521 -1 O VAL A 517 N PHE A 49 SHEET 3 B 4 HIS A 508 SER A 513 -1 N LEU A 509 O VAL A 520 SHEET 4 B 4 SER A 503 LEU A 505 -1 N SER A 503 O LEU A 510 SHEET 1 C 4 VAL A 55 GLU A 62 0 SHEET 2 C 4 SER A 68 ILE A 74 -1 O PHE A 71 N VAL A 59 SHEET 3 C 4 ARG A 77 LEU A 81 -1 O HIS A 79 N VAL A 72 SHEET 4 C 4 SER A 87 ALA A 92 -1 O VAL A 88 N VAL A 80 SHEET 1 D 4 THR A 120 ASP A 126 0 SHEET 2 D 4 ALA A 131 GLY A 136 -1 O ALA A 131 N ASP A 126 SHEET 3 D 4 CYS A 143 GLN A 151 -1 O HIS A 146 N LEU A 132 SHEET 4 D 4 ALA A 154 LEU A 157 -1 O HIS A 156 N GLU A 149 SHEET 1 E 4 THR A 120 ASP A 126 0 SHEET 2 E 4 ALA A 131 GLY A 136 -1 O ALA A 131 N ASP A 126 SHEET 3 E 4 CYS A 143 GLN A 151 -1 O HIS A 146 N LEU A 132 SHEET 4 E 4 ALA A 161 CYS A 162 -1 O ALA A 161 N LEU A 145 SHEET 1 F 4 THR A 184 GLN A 191 0 SHEET 2 F 4 ALA A 194 SER A 201 -1 O TYR A 198 N THR A 187 SHEET 3 F 4 VAL A 216 ARG A 220 -1 O ARG A 219 N PHE A 197 SHEET 4 F 4 VAL A 233 LEU A 235 -1 O LEU A 235 N VAL A 216 SHEET 1 G 5 GLU A 248 THR A 255 0 SHEET 2 G 5 PHE A 258 PRO A 266 -1 O VAL A 264 N GLU A 248 SHEET 3 G 5 LEU A 276 SER A 284 -1 O ALA A 281 N PHE A 261 SHEET 4 G 5 ARG A 294 PHE A 302 -1 O ARG A 294 N ARG A 282 SHEET 5 G 5 LEU A 427 LEU A 428 1 O LEU A 427 N GLU A 295 SHEET 1 H 3 GLN A 316 TYR A 318 0 SHEET 2 H 3 ARG A 294 PHE A 302 -1 N PHE A 302 O GLN A 316 SHEET 3 H 3 PHE A 433 VAL A 436 1 O PHE A 433 N ASP A 299 SHEET 1 I 3 VAL A 320 PRO A 328 0 SHEET 2 I 3 GLU A 344 VAL A 351 -1 O VAL A 349 N GLN A 322 SHEET 3 I 3 VAL A 365 PRO A 370 -1 O PHE A 369 N LEU A 346 SHEET 1 J 2 GLY A 546 TRP A 547 0 SHEET 2 J 2 CYS A 552 GLY A 553 -1 O GLY A 553 N GLY A 546 SSBOND 1 CYS A 101 CYS A 104 1555 1555 2.07 SSBOND 2 CYS A 107 CYS A 162 1555 1555 2.14 SSBOND 3 CYS A 135 CYS A 143 1555 1555 2.03 SSBOND 4 CYS A 174 CYS A 177 1555 1555 2.01 SSBOND 5 CYS A 300 CYS A 367 1555 1555 2.00 SSBOND 6 CYS A 385 CYS A 407 1555 1555 2.05 SSBOND 7 CYS A 386 CYS A 422 1555 1555 2.06 SSBOND 8 CYS A 527 CYS A 545 1555 1555 2.04 SSBOND 9 CYS A 533 CYS A 567 1555 1555 2.05 SSBOND 10 CYS A 536 CYS A 552 1555 1555 2.04 SSBOND 11 CYS A 548 CYS A 558 1555 1555 2.01 LINK ND2 ASN A 488 C1 NAG B 1 1555 1555 1.41 LINK O4 NAG B 1 C1 NAG B 2 1555 1555 1.42 LINK O4 NAG B 2 C1 BMA B 3 1555 1555 1.44 LINK O3 BMA B 3 C1 BMA B 4 1555 1555 1.45 CISPEP 1 GLY A 94 PRO A 95 0 -1.71 CISPEP 2 GLY A 110 PRO A 111 0 -24.17 CISPEP 3 GLY A 113 PRO A 114 0 -7.82 CISPEP 4 LEU A 129 PRO A 130 0 -12.10 CISPEP 5 CYS A 407 PRO A 408 0 7.41 CRYST1 106.400 73.300 87.900 90.00 97.40 90.00 C 1 2 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 0.009398 0.000000 0.001221 0.00000 SCALE2 0.000000 0.013643 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011472 0.00000