HEADER HORMONE 23-OCT-10 2XV7 TITLE CRYSTAL STRUCTURE OF VASCULAR ENDOTHELIAL GROWTH FACTOR D COMPND MOL_ID: 1; COMPND 2 MOLECULE: VASCULAR ENDOTHELIAL GROWTH FACTOR D; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: VEGF HOMOLOGY DOMAIN, RESIDUES 92-195; COMPND 5 SYNONYM: C-FOS-INDUCED GROWTH FACTOR, VEGF-D, FIGF; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 OTHER_DETAILS: N-GLYCOSYLATION AT ASN155 AND ASN185. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: SF21; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PFASTBAC KEYWDS ANGIOGENESIS, LYMPHANGIOGENESIS, HORMONE EXPDTA X-RAY DIFFRACTION AUTHOR V.-M.LEPPANEN,M.JELTSCH,A.ANISIMOV,D.TVOROGOV,K.AHO,N.KALKKINEN, AUTHOR 2 P.TOIVANEN,S.YLA-HERTTUALA,K.BALLMER-HOFER,K.ALITALO REVDAT 4 20-DEC-23 2XV7 1 HETSYN REVDAT 3 29-JUL-20 2XV7 1 COMPND REMARK HETNAM LINK REVDAT 3 2 1 SITE ATOM REVDAT 2 06-APR-11 2XV7 1 JRNL REVDAT 1 12-JAN-11 2XV7 0 JRNL AUTH V.M.LEPPANEN,M.JELTSCH,A.ANISIMOV,D.TVOROGOV,K.AHO, JRNL AUTH 2 N.KALKKINEN,P.TOIVANEN,S.YLA-HERTTUALA,K.BALLMER-HOFER, JRNL AUTH 3 K.ALITALO JRNL TITL STRUCTURAL DETERMINANTS OF VASCULAR ENDOTHELIAL GROWTH JRNL TITL 2 FACTOR-D - RECEPTOR BINDING AND SPECIFICITY. JRNL REF BLOOD V. 117 1507 2011 JRNL REFN ISSN 0006-4971 JRNL PMID 21148085 JRNL DOI 10.1182/BLOOD-2010-08-301549 REMARK 2 REMARK 2 RESOLUTION. 2.90 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) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.89 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.990 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 4543 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.263 REMARK 3 R VALUE (WORKING SET) : 0.255 REMARK 3 FREE R VALUE : 0.333 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 454 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 19.8930 - 4.1742 1.00 1432 160 0.2362 0.3122 REMARK 3 2 4.1742 - 3.3181 1.00 1348 149 0.2410 0.3476 REMARK 3 3 3.3181 - 2.9002 0.99 1309 145 0.3392 0.3645 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 : 0.26 REMARK 3 B_SOL : 64.07 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.470 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.680 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 67.19 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 81.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.83260 REMARK 3 B22 (A**2) : 2.83260 REMARK 3 B33 (A**2) : -5.66510 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 : 0.010 900 REMARK 3 ANGLE : 1.543 1230 REMARK 3 CHIRALITY : 0.089 166 REMARK 3 PLANARITY : 0.011 143 REMARK 3 DIHEDRAL : 33.883 356 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN A AND RESID 91:194) REMARK 3 ORIGIN FOR THE GROUP (A): -30.5644 -30.3984 -3.3104 REMARK 3 T TENSOR REMARK 3 T11: 0.4331 T22: -0.0098 REMARK 3 T33: 0.1665 T12: -0.0204 REMARK 3 T13: 0.1903 T23: 0.0495 REMARK 3 L TENSOR REMARK 3 L11: 1.7173 L22: 1.8608 REMARK 3 L33: 1.1530 L12: -0.0933 REMARK 3 L13: -0.7178 L23: -2.5154 REMARK 3 S TENSOR REMARK 3 S11: 0.4120 S12: -0.0494 S13: 0.3517 REMARK 3 S21: 0.2779 S22: 0.1999 S23: 0.0282 REMARK 3 S31: -0.0193 S32: 0.2670 S33: -0.3788 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESID 400:404) REMARK 3 ORIGIN FOR THE GROUP (A): -31.6475 -14.3973 0.0723 REMARK 3 T TENSOR REMARK 3 T11: 1.6103 T22: 0.5742 REMARK 3 T33: 0.8548 T12: 0.4396 REMARK 3 T13: 0.2078 T23: 0.0076 REMARK 3 L TENSOR REMARK 3 L11: 0.9281 L22: 5.0111 REMARK 3 L33: 0.3538 L12: 0.1498 REMARK 3 L13: -0.2518 L23: -1.1844 REMARK 3 S TENSOR REMARK 3 S11: -0.3513 S12: -0.0885 S13: 1.0855 REMARK 3 S21: 0.2769 S22: -0.2072 S23: -1.0457 REMARK 3 S31: -1.7349 S32: -0.4917 S33: -0.3324 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN A AND RESID 500:502) REMARK 3 ORIGIN FOR THE GROUP (A): -19.1024 -32.8560 3.5458 REMARK 3 T TENSOR REMARK 3 T11: 0.1854 T22: 0.8643 REMARK 3 T33: 1.0574 T12: -0.1873 REMARK 3 T13: -0.0562 T23: -0.0684 REMARK 3 L TENSOR REMARK 3 L11: 2.0163 L22: 3.8979 REMARK 3 L33: 9.1842 L12: -7.3551 REMARK 3 L13: 3.5174 L23: -4.4129 REMARK 3 S TENSOR REMARK 3 S11: 0.0581 S12: 0.1385 S13: -3.3127 REMARK 3 S21: 0.0746 S22: -0.2298 S23: -0.5304 REMARK 3 S31: -0.7080 S32: 1.9172 S33: 0.1628 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE SIDECHAINS OF THE RESIDUES TYR94, REMARK 3 GLU97, LYS126, SER127, ASN129, SER169, VAL70, THR173, AND LYS190 REMARK 3 ARE DISORDERED AND THE SIDECHAIN ATOMS WERE OMITTED FROM THE REMARK 3 REFINEMENT. REMARK 4 REMARK 4 2XV7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 23-OCT-10. REMARK 100 THE DEPOSITION ID IS D_1290045786. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-MAY-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00 REMARK 200 MONOCHROMATOR : SI(111) MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36742 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900 REMARK 200 RESOLUTION RANGE LOW (A) : 80.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 8.800 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 9.20 REMARK 200 R MERGE FOR SHELL (I) : 0.77000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: VEGF-C FROM PDB ENTRY 2X1W REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: A SINGLE VEGF-D CRYSTAL GREW IN 6 REMARK 280 WEEKS AT ROOM TEMPERATURE OVER A RESERVOIR SOLUTION OF 0.1 M REMARK 280 PHOSPHATE/CITRATE BUFFER AT PH 4.2, 40 % ETHANOL (V/V), 5 % PEG REMARK 280 1000 (W/V). REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+5/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 23.64667 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 47.29333 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 35.47000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 59.11667 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 11.82333 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 23.64667 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 47.29333 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 59.11667 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 35.47000 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 11.82333 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4960 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15170 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 21.6 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 BIOMT1 2 0.500000 -0.866025 0.000000 -47.86000 REMARK 350 BIOMT2 2 -0.866025 -0.500000 0.000000 -82.89595 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -11.82333 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A2010 LIES ON A SPECIAL POSITION. REMARK 400 REMARK 400 COMPOUND REMARK 400 ENGINEERED RESIDUE IN CHAIN A, CYS 117 TO ALA 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 ASP A 90 REMARK 465 ALA A 195 REMARK 465 HIS A 196 REMARK 465 HIS A 197 REMARK 465 HIS A 198 REMARK 465 HIS A 199 REMARK 465 HIS A 200 REMARK 465 HIS A 201 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 TYR A 94 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 GLU A 97 CG CD OE1 OE2 REMARK 470 LYS A 126 CG CD CE NZ REMARK 470 SER A 127 OG REMARK 470 ASN A 129 CG OD1 ND2 REMARK 470 SER A 169 CB OG REMARK 470 VAL A 170 CG1 CG2 REMARK 470 THR A 173 OG1 CG2 REMARK 470 LYS A 190 CG CD CE NZ 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 SER A 112 CB SER A 112 OG 0.090 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 99 CA - CB - CG ANGL. DEV. = -14.8 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 LYS A 100 -72.03 -22.06 REMARK 500 LEU A 172 -41.12 -161.44 REMARK 500 VAL A 175 138.75 69.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 MAN A 403 REMARK 610 MAN A 404 REMARK 999 REMARK 999 SEQUENCE REMARK 999 FIRST TWO RESIDUES (ASP, PRO) ARE CLONING ARTEFACTS AND REMARK 999 THERE IS A C-TERMINAL HEXAHISTIDINE TAG. DBREF 2XV7 A 92 195 UNP O43915 VEGFD_HUMAN 92 195 SEQADV 2XV7 ASP A 90 UNP O43915 EXPRESSION TAG SEQADV 2XV7 PRO A 91 UNP O43915 EXPRESSION TAG SEQADV 2XV7 ALA A 117 UNP O43915 CYS 117 ENGINEERED MUTATION SEQADV 2XV7 HIS A 196 UNP O43915 EXPRESSION TAG SEQADV 2XV7 HIS A 197 UNP O43915 EXPRESSION TAG SEQADV 2XV7 HIS A 198 UNP O43915 EXPRESSION TAG SEQADV 2XV7 HIS A 199 UNP O43915 EXPRESSION TAG SEQADV 2XV7 HIS A 200 UNP O43915 EXPRESSION TAG SEQADV 2XV7 HIS A 201 UNP O43915 EXPRESSION TAG SEQRES 1 A 112 ASP PRO THR PHE TYR ASP ILE GLU THR LEU LYS VAL ILE SEQRES 2 A 112 ASP GLU GLU TRP GLN ARG THR GLN CYS SER PRO ARG GLU SEQRES 3 A 112 THR ALA VAL GLU VAL ALA SER GLU LEU GLY LYS SER THR SEQRES 4 A 112 ASN THR PHE PHE LYS PRO PRO CYS VAL ASN VAL PHE ARG SEQRES 5 A 112 CYS GLY GLY CYS CYS ASN GLU GLU SER LEU ILE CYS MET SEQRES 6 A 112 ASN THR SER THR SER TYR ILE SER LYS GLN LEU PHE GLU SEQRES 7 A 112 ILE SER VAL PRO LEU THR SER VAL PRO GLU LEU VAL PRO SEQRES 8 A 112 VAL LYS VAL ALA ASN HIS THR GLY CYS LYS CYS LEU PRO SEQRES 9 A 112 THR ALA HIS HIS HIS HIS HIS HIS MODRES 2XV7 ASN A 155 ASN GLYCOSYLATION SITE MODRES 2XV7 ASN A 185 ASN GLYCOSYLATION SITE HET NAG B 1 14 HET NAG B 2 14 HET BMA B 3 11 HET NAG C 1 14 HET NAG C 2 14 HET BMA C 3 11 HET MAN A 403 11 HET MAN A 404 11 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM BMA BETA-D-MANNOPYRANOSE HETNAM MAN ALPHA-D-MANNOPYRANOSE 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 MAN ALPHA-D-MANNOSE; D-MANNOSE; MANNOSE FORMUL 2 NAG 4(C8 H15 N O6) FORMUL 2 BMA 2(C6 H12 O6) FORMUL 4 MAN 2(C6 H12 O6) FORMUL 6 HOH *13(H2 O) HELIX 1 1 THR A 92 THR A 109 1 18 HELIX 2 2 ALA A 121 LEU A 124 5 4 HELIX 3 3 LYS A 126 ASN A 129 5 4 SHEET 1 AA 2 SER A 112 GLU A 119 0 SHEET 2 AA 2 CYS A 136 GLY A 143 -1 O VAL A 137 N VAL A 118 SHEET 1 AB 2 ILE A 152 PHE A 166 0 SHEET 2 AB 2 LEU A 178 LEU A 192 -1 O VAL A 179 N LEU A 165 SSBOND 1 CYS A 111 CYS A 153 1555 1555 2.04 SSBOND 2 CYS A 136 CYS A 145 1555 10444 2.03 SSBOND 3 CYS A 142 CYS A 189 1555 1555 2.04 SSBOND 4 CYS A 146 CYS A 191 1555 1555 2.04 LINK ND2 ASN A 155 C1 NAG B 1 1555 1555 1.46 LINK ND2 ASN A 185 C1 NAG C 1 1555 1555 1.44 LINK O4 NAG B 1 C1 NAG B 2 1555 1555 1.44 LINK O4 NAG B 2 C1 BMA B 3 1555 1555 1.43 LINK O4 NAG C 1 C1 NAG C 2 1555 1555 1.44 LINK O4 NAG C 2 C1 BMA C 3 1555 1555 1.45 CISPEP 1 LYS A 133 PRO A 134 0 -3.38 CISPEP 2 VAL A 170 PRO A 171 0 -10.31 CISPEP 3 PRO A 171 LEU A 172 0 -1.97 CISPEP 4 THR A 173 SER A 174 0 5.86 CISPEP 5 PRO A 193 THR A 194 0 -10.92 CRYST1 95.720 95.720 70.940 90.00 90.00 120.00 P 61 2 2 12 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 0.010447 0.006032 0.000000 0.00000 SCALE2 0.000000 0.012063 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014096 0.00000