HEADER HORMONE/GROWTH FACTOR 28-AUG-02 1MJV TITLE DISULFIDE DEFICIENT MUTANT OF VASCULAR ENDOTHELIAL GROWTH FACTOR A TITLE 2 (C51A AND C60A) COMPND MOL_ID: 1; COMPND 2 MOLECULE: VASCULAR ENDOTHELIAL GROWTH FACTOR A; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: RESIDUES 40-134, SEQUENCE DATABASE; COMPND 5 SYNONYM: VEGF-A, VASCULAR PERMEABILITY FACTOR, VPF; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: B843(DE3)PLYSS; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET-3D KEYWDS CYSTINE-KNOT GROWTH FACTOR, HORMONE-GROWTH FACTOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Y.A.MULLER,C.HEIRING,R.MISSELWITZ,K.WELFLE,H.WELFLE REVDAT 5 27-OCT-21 1MJV 1 SEQADV REVDAT 4 04-APR-18 1MJV 1 REMARK REVDAT 3 11-OCT-17 1MJV 1 REMARK REVDAT 2 24-FEB-09 1MJV 1 VERSN REVDAT 1 11-DEC-02 1MJV 0 JRNL AUTH Y.A.MULLER,C.HEIRING,R.MISSELWITZ,K.WELFLE,H.WELFLE JRNL TITL THE CYSTINE KNOT PROMOTES FOLDING AND NOT THERMODYNAMIC JRNL TITL 2 STABILITY IN VASCULAR ENDOTHELIAL GROWTH FACTOR JRNL REF J.BIOL.CHEM. V. 277 43410 2002 JRNL REFN ISSN 0021-9258 JRNL PMID 12207021 JRNL DOI 10.1074/JBC.M206438200 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH C.HEIRING,Y.A.MULLER REMARK 1 TITL FOLDING SCREENING ASSAYED BY PROTEOLYSIS: APPLICATION TO REMARK 1 TITL 2 VARIOUS CYSTINE DELETION MUTANTS OF VASCULAR ENDOTHELIAL REMARK 1 TITL 3 GROWTH FACTOR REMARK 1 REF PROTEIN ENG. V. 14 183 2001 REMARK 1 REFN ISSN 0269-2139 REMARK 1 DOI 10.1093/PROTEIN/14.3.183 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 12713 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : R-FREE REMARK 3 FREE R VALUE TEST SET SELECTION : RESOLUTION SPHERES REMARK 3 R VALUE (WORKING SET) : 0.196 REMARK 3 FREE R VALUE : 0.248 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1406 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1540 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 211 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -7.17400 REMARK 3 B22 (A**2) : 7.47300 REMARK 3 B33 (A**2) : -0.29900 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -7.85500 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.100 REMARK 3 BOND ANGLES (DEGREES) : 1.500 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1MJV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-AUG-02. REMARK 100 THE DEPOSITION ID IS D_1000016967. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-JUN-00 REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : MIRRORS REMARK 200 OPTICS : OSMICS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14119 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 19.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.06800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.20 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.36 REMARK 200 R MERGE FOR SHELL (I) : 0.27400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 2VPF REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.21 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.75 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NA-CITRATE, ISOPROPANOL, PEG4000, PH REMARK 280 5.6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K 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 38.60000 REMARK 290 SMTRY3 2 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2370 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11570 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -19.0 KCAL/MOL 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 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 MET A 13 CG SD CE REMARK 470 LYS A 108 CG CD CE NZ REMARK 470 MET B 13 CG SD CE REMARK 470 LYS B 108 CG CD CE NZ 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 A 26 113.97 -27.39 REMARK 500 GLU A 64 -10.10 -48.13 REMARK 500 HIS A 86 -7.06 74.69 REMARK 500 CYS B 26 122.52 -24.41 REMARK 500 PRO B 85 132.68 -32.85 REMARK 500 GLN B 87 0.59 -156.47 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2VPF RELATED DB: PDB REMARK 900 VASCULAR ENDOTHELIAL GROWTH FACTOR REFINED TO 1.93 ANGSTROMS REMARK 900 RESOLUTION REMARK 900 RELATED ID: 1MKG RELATED DB: PDB REMARK 900 DISULFIDE DEFICIENT MUTANT OF VASCULAR ENDOTHELIAL GROWTH FACTOR A REMARK 900 (C57A AND C102A) REMARK 900 RELATED ID: 1MKK RELATED DB: PDB REMARK 900 DISULFIDE DEFICIENT MUTANT OF VASCULAR ENDOTHELIAL GROWTH FACTOR A REMARK 900 (C61A AND C104A) DBREF 1MJV A 14 108 UNP P15692 VEGFA_HUMAN 40 134 DBREF 1MJV B 14 108 UNP P15692 VEGFA_HUMAN 40 134 SEQADV 1MJV MET A 13 UNP P15692 CLONING ARTIFACT SEQADV 1MJV ALA A 51 UNP P15692 CYS 77 ENGINEERED MUTATION SEQADV 1MJV ALA A 60 UNP P15692 CYS 86 ENGINEERED MUTATION SEQADV 1MJV MET B 13 UNP P15692 CLONING ARTIFACT SEQADV 1MJV ALA B 51 UNP P15692 CYS 77 ENGINEERED MUTATION SEQADV 1MJV ALA B 60 UNP P15692 CYS 86 ENGINEERED MUTATION SEQRES 1 A 96 MET VAL VAL LYS PHE MET ASP VAL TYR GLN ARG SER TYR SEQRES 2 A 96 CYS HIS PRO ILE GLU THR LEU VAL ASP ILE PHE GLN GLU SEQRES 3 A 96 TYR PRO ASP GLU ILE GLU TYR ILE PHE LYS PRO SER ALA SEQRES 4 A 96 VAL PRO LEU MET ARG CYS GLY GLY ALA CYS ASN ASP GLU SEQRES 5 A 96 GLY LEU GLU CYS VAL PRO THR GLU GLU SER ASN ILE THR SEQRES 6 A 96 MET GLN ILE MET ARG ILE LYS PRO HIS GLN GLY GLN HIS SEQRES 7 A 96 ILE GLY GLU MET SER PHE LEU GLN HIS ASN LYS CYS GLU SEQRES 8 A 96 CYS ARG PRO LYS LYS SEQRES 1 B 96 MET VAL VAL LYS PHE MET ASP VAL TYR GLN ARG SER TYR SEQRES 2 B 96 CYS HIS PRO ILE GLU THR LEU VAL ASP ILE PHE GLN GLU SEQRES 3 B 96 TYR PRO ASP GLU ILE GLU TYR ILE PHE LYS PRO SER ALA SEQRES 4 B 96 VAL PRO LEU MET ARG CYS GLY GLY ALA CYS ASN ASP GLU SEQRES 5 B 96 GLY LEU GLU CYS VAL PRO THR GLU GLU SER ASN ILE THR SEQRES 6 B 96 MET GLN ILE MET ARG ILE LYS PRO HIS GLN GLY GLN HIS SEQRES 7 B 96 ILE GLY GLU MET SER PHE LEU GLN HIS ASN LYS CYS GLU SEQRES 8 B 96 CYS ARG PRO LYS LYS FORMUL 3 HOH *211(H2 O) HELIX 1 1 LYS A 16 TYR A 25 1 10 HELIX 2 2 ILE A 35 TYR A 39 1 5 HELIX 3 3 LYS B 16 TYR B 25 1 10 HELIX 4 4 ILE B 35 TYR B 39 1 5 SHEET 1 A 2 HIS A 27 ASP A 34 0 SHEET 2 A 2 ALA A 51 GLY A 58 -1 O LEU A 54 N THR A 31 SHEET 1 B 3 ILE A 46 LYS A 48 0 SHEET 2 B 3 LEU A 66 ILE A 83 -1 O ILE A 83 N ILE A 46 SHEET 3 B 3 GLN A 89 PRO A 106 -1 O HIS A 90 N ARG A 82 SHEET 1 C 2 HIS B 27 ASP B 34 0 SHEET 2 C 2 ALA B 51 GLY B 58 -1 O LEU B 54 N THR B 31 SHEET 1 D 3 ILE B 46 LYS B 48 0 SHEET 2 D 3 LEU B 66 ILE B 83 -1 O ILE B 83 N ILE B 46 SHEET 3 D 3 GLN B 89 PRO B 106 -1 O GLY B 92 N ILE B 80 SSBOND 1 CYS A 26 CYS A 68 1555 1555 2.04 SSBOND 2 CYS A 57 CYS A 102 1555 1555 2.02 SSBOND 3 CYS A 61 CYS A 104 1555 1555 2.02 SSBOND 4 CYS B 26 CYS B 68 1555 1555 2.01 SSBOND 5 CYS B 57 CYS B 102 1555 1555 2.03 SSBOND 6 CYS B 61 CYS B 104 1555 1555 2.03 CISPEP 1 LYS A 48 PRO A 49 0 -0.20 CISPEP 2 LYS B 48 PRO B 49 0 -0.72 CRYST1 29.280 77.200 55.110 90.00 98.92 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 0.034153 0.000000 0.005360 0.00000 SCALE2 0.000000 0.012953 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018368 0.00000