HEADER HORMONE/GROWTH FACTOR 11-MAY-01 1IMX
TITLE 1.8 ANGSTROM CRYSTAL STRUCTURE OF IGF-1
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: INSULIN-LIKE GROWTH FACTOR 1A;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: IGF-1;
COMPND 5 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: IGF-1;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS INSULIN/RELAXIN, DETERGENT, HORMONE/GROWTH FACTOR COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR F.F.VAJDOS,M.ULTSCH,M.L.SCHAFFER,K.D.DESHAYES,J.LIU,
AUTHOR 2 N.J.SKELTON,A.M.DE VOS
REVDAT 3 24-FEB-09 1IMX 1 VERSN
REVDAT 2 03-OCT-01 1IMX 1 JRNL
REVDAT 1 05-SEP-01 1IMX 0
JRNL AUTH F.F.VAJDOS,M.ULTSCH,M.L.SCHAFFER,K.D.DESHAYES,
JRNL AUTH 2 J.LIU,N.J.SKELTON,A.M.DE VOS
JRNL TITL CRYSTAL STRUCTURE OF HUMAN INSULIN-LIKE GROWTH
JRNL TITL 2 FACTOR-1: DETERGENT BINDING INHIBITS BINDING
JRNL TITL 3 PROTEIN INTERACTIONS.
JRNL REF BIOCHEMISTRY V. 40 11022 2001
JRNL REFN ISSN 0006-2960
JRNL PMID 11551198
JRNL DOI 10.1021/BI0109111
REMARK 1
REMARK 2
REMARK 2 RESOLUTION. 1.82 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : CNX 2000
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 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.82
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.00
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 864194.510
REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000
REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.9
REMARK 3 NUMBER OF REFLECTIONS : 6871
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) : NULL
REMARK 3 R VALUE (WORKING SET) : 0.245
REMARK 3 FREE R VALUE : 0.258
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.100
REMARK 3 FREE R VALUE TEST SET COUNT : 558
REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.011
REMARK 3
REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA.
REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL
REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL
REMARK 3 FREE R VALUE (NO CUTOFF) : NULL
REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL
REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL
REMARK 3 ESTIMATED ERROR OF FREE R VALUE (NO CUTOFF) : NULL
REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 7015
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) : 1.80
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.91
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 74.60
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 825
REMARK 3 BIN R VALUE (WORKING SET) : 0.2740
REMARK 3 BIN FREE R VALUE : 0.3350
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 6.10
REMARK 3 BIN FREE R VALUE TEST SET COUNT : 54
REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.046
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 431
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 61
REMARK 3 SOLVENT ATOMS : 47
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 26.20
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.80
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -3.68000
REMARK 3 B22 (A**2) : -1.65000
REMARK 3 B33 (A**2) : 5.33000
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) : 0.24
REMARK 3 ESD FROM SIGMAA (A) : 0.12
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) : 0.27
REMARK 3 ESD FROM C-V SIGMAA (A) : 0.17
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 BOND LENGTHS (A) : 0.009
REMARK 3 BOND ANGLES (DEGREES) : 1.20
REMARK 3 DIHEDRAL ANGLES (DEGREES) : 20.20
REMARK 3 IMPROPER ANGLES (DEGREES) : 0.75
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) : 1.860 ; 1.500
REMARK 3 MAIN-CHAIN ANGLE (A**2) : 3.160 ; 2.000
REMARK 3 SIDE-CHAIN BOND (A**2) : 2.680 ; 2.000
REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.210 ; 2.500
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 PARAMETER FILE 1 : PROTEIN_REP.PARAM
REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM
REMARK 3 PARAMETER FILE 3 : ION.PARAM
REMARK 3 PARAMETER FILE 4 : DBC.PAR
REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP
REMARK 3 TOPOLOGY FILE 2 : WATER.TOP
REMARK 3 TOPOLOGY FILE 3 : ION.TOP
REMARK 3 TOPOLOGY FILE 4 : DBC.TOP
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 1IMX COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-MAY-01.
REMARK 100 THE RCSB ID CODE IS RCSB013417.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 04-JAN-01
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 6.5
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : SSRL
REMARK 200 BEAMLINE : BL9-2
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.9197, 1.5406, 0.9199, 0.8610
REMARK 200 MONOCHROMATOR : DOUBLE-CRYSTAL MONOCHROMATOR
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO
REMARK 200 DATA SCALING SOFTWARE : SCALEPACK
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6871
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.820
REMARK 200 RESOLUTION RANGE LOW (A) : 20.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4
REMARK 200 DATA REDUNDANCY : 1.800
REMARK 200 R MERGE (I) : 0.03800
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.7000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.83
REMARK 200 COMPLETENESS FOR SHELL (%) : 99.1
REMARK 200 DATA REDUNDANCY IN SHELL : 1.80
REMARK 200 R MERGE FOR SHELL (I) : 0.29000
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.500
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: MAD
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD
REMARK 200 SOFTWARE USED: SHARP
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 49.45
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.43
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, DEOXY BIG CHAPS, SODIUM
REMARK 280 CACODYLATE, PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE
REMARK 280 293K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,-Y,Z+1/2
REMARK 290 3555 -X,Y,-Z+1/2
REMARK 290 4555 X,-Y,-Z
REMARK 290 5555 X+1/2,Y+1/2,Z
REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2
REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2
REMARK 290 8555 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 32.99800
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 32.99800
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 0.00000
REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 15.91550
REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 35.52750
REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 15.91550
REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 35.52750
REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 32.99800
REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 15.91550
REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 35.52750
REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 32.99800
REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 15.91550
REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 35.52750
REMARK 290 SMTRY3 8 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 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 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 GLY A 1
REMARK 465 PRO A 2
REMARK 465 SER A 35
REMARK 465 ARG A 36
REMARK 465 ARG A 37
REMARK 465 ALA A 38
REMARK 465 PRO A 39
REMARK 465 GLN A 40
REMARK 465 LYS A 65
REMARK 465 PRO A 66
REMARK 465 ALA A 67
REMARK 465 LYS A 68
REMARK 465 SER A 69
REMARK 465 ALA A 70
REMARK 525
REMARK 525 SOLVENT
REMARK 525
REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT
REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST
REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT
REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE
REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER;
REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE
REMARK 525 NUMBER; I=INSERTION CODE):
REMARK 525
REMARK 525 M RES CSSEQI
REMARK 525 HOH A 218 DISTANCE = 6.04 ANGSTROMS
REMARK 525 HOH A 225 DISTANCE = 5.95 ANGSTROMS
REMARK 525 HOH A 227 DISTANCE = 6.42 ANGSTROMS
REMARK 525 HOH A 238 DISTANCE = 7.04 ANGSTROMS
REMARK 525 HOH A 242 DISTANCE = 6.23 ANGSTROMS
REMARK 525 HOH A 243 DISTANCE = 6.32 ANGSTROMS
REMARK 615
REMARK 615 ZERO OCCUPANCY ATOM
REMARK 615 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO
REMARK 615 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS
REMARK 615 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME;
REMARK 615 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 615 M RES C SSEQI
REMARK 615 CPQ A 101
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BR A 201
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CPQ A 101
DBREF 1IMX A 1 70 UNP P01343 IGF1A_HUMAN 49 118
SEQRES 1 A 70 GLY PRO GLU THR LEU CYS GLY ALA GLU LEU VAL ASP ALA
SEQRES 2 A 70 LEU GLN PHE VAL CYS GLY ASP ARG GLY PHE TYR PHE ASN
SEQRES 3 A 70 LYS PRO THR GLY TYR GLY SER SER SER ARG ARG ALA PRO
SEQRES 4 A 70 GLN THR GLY ILE VAL ASP GLU CYS CYS PHE ARG SER CYS
SEQRES 5 A 70 ASP LEU ARG ARG LEU GLU MET TYR CYS ALA PRO LEU LYS
SEQRES 6 A 70 PRO ALA LYS SER ALA
HET BR A 201 1
HET CPQ A 101 60
HETNAM BR BROMIDE ION
HETNAM CPQ N,N-BIS(3-D-GLUCONAMIDOPROPYL)DEOXYCHOLAMIDE
HETSYN CPQ DEOXY-BIGCHAP
FORMUL 2 BR BR 1-
FORMUL 3 CPQ C42 H75 N3 O15
FORMUL 4 HOH *47(H2 O)
HELIX 1 1 CYS A 6 GLY A 19 1 14
HELIX 2 2 GLY A 42 CYS A 48 1 7
HELIX 3 3 ASP A 53 MET A 59 1 7
SSBOND 1 CYS A 6 CYS A 48 1555 1555 2.03
SSBOND 2 CYS A 18 CYS A 61 1555 1555 2.03
SSBOND 3 CYS A 47 CYS A 52 1555 1555 2.03
SITE 1 AC1 3 TYR A 24 PHE A 25 ASN A 26
SITE 1 AC2 13 GLU A 3 THR A 4 LEU A 5 GLN A 15
SITE 2 AC2 13 PHE A 16 PHE A 25 TYR A 31 ARG A 50
SITE 3 AC2 13 CYS A 52 HOH A 203 HOH A 204 HOH A 212
SITE 4 AC2 13 HOH A 215
CRYST1 31.831 71.055 65.996 90.00 90.00 90.00 C 2 2 21 8
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 0.031416 0.000000 0.000000 0.00000
SCALE2 0.000000 0.014074 0.000000 0.00000
SCALE3 0.000000 0.000000 0.015152 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
