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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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
(ATOM LINES ARE NOT SHOWN.)
END
