PDB Short entry for 2GMF HEADER GROWTH FACTOR 24-APR-96 2GMF TITLE HUMAN GRANULOCYTE MACROPHAGE COLONY STIMULATING FACTOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: GRANULOCYTE-MACROPHAGE COLONY-STIMULATING FACTOR; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: 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 KEYWDS GRANULOCYTE-MACROPHAGE COLONY STIMULATING GROWTH FACTOR EXPDTA X-RAY DIFFRACTION AUTHOR D.ROZWARSKI,K.DIEDERICHS,R.HECHT,T.BOONE,P.A.KARPLUS REVDAT 2 24-FEB-09 2GMF 1 VERSN REVDAT 1 08-NOV-96 2GMF 0 SPRSDE 08-NOV-96 2GMF 1GMF JRNL AUTH D.A.ROZWARSKI,K.DIEDERICHS,R.HECHT,T.BOONE, JRNL AUTH 2 P.A.KARPLUS JRNL TITL REFINED CRYSTAL STRUCTURE AND MUTAGENESIS OF HUMAN JRNL TITL 2 GRANULOCYTE-MACROPHAGE COLONY-STIMULATING FACTOR. JRNL REF PROTEINS V. 26 304 1996 JRNL REFN ISSN 0887-3585 JRNL PMID 8953651 JRNL DOI 10.1002/(SICI)1097-0134(199611)26:3<304::AID-PROT6> JRNL DOI 2 3.0.CO;2-D REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH K.DIEDERICHS,T.BOONE,P.A.KARPLUS REMARK 1 TITL NOVEL FOLD AND PUTATIVE RECEPTOR BINDING SITE OF REMARK 1 TITL 2 GRANULOCYTE-MACROPHAGE COLONY-STIMULATING FACTOR REMARK 1 REF SCIENCE V. 254 1779 1991 REMARK 1 REFN ISSN 0036-8075 REMARK 1 REFERENCE 2 REMARK 1 AUTH K.DIEDERICHS,S.JACQUES,T.BOONE,P.A.KARPLUS REMARK 1 TITL LOW-RESOLUTION STRUCTURE OF RECOMBINANT HUMAN REMARK 1 TITL 2 GRANULOCYTE-MACROPHAGE COLONY STIMULATING FACTOR REMARK 1 REF J.MOL.BIOL. V. 221 55 1991 REMARK 1 REFN ISSN 0022-2836 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 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) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 19868 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.235 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL 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 : 1937 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 92 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.30 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) : 0.013 REMARK 3 BOND ANGLES (DEGREES) : 1.60 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.50 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 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: PRO A 124 IS VERY MOBILE. THE REMARK 3 PEPTIDE BOND PRECEDING IT IS NOT RELIABLY REFINED. PRO A 124 REMARK 3 IS VERY MOBILE. THE PEPTIDE BOND PRECEDING IT IS NOT RELIABLY REMARK 3 REFINED. REMARK 4 REMARK 4 2GMF COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: X-PLOR 3.1 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.73 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.05 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 23.76000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 63.14500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.53000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 63.14500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.76000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.53000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 ALA A 1 REMARK 465 PRO A 2 REMARK 465 ALA A 3 REMARK 465 VAL A 125 REMARK 465 GLN A 126 REMARK 465 GLU A 127 REMARK 465 ALA B 1 REMARK 465 PRO B 2 REMARK 465 ALA B 3 REMARK 465 PRO B 124 REMARK 465 VAL B 125 REMARK 465 GLN B 126 REMARK 465 GLU B 127 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 SER A 5 51.70 -170.88 REMARK 500 PRO A 8 -16.33 -45.68 REMARK 500 SER A 29 127.36 -34.20 REMARK 500 GLU A 93 56.70 -102.72 REMARK 500 SER A 95 74.56 -107.03 REMARK 500 ASP A 120 -94.91 -108.41 REMARK 500 CYS A 121 -148.03 -142.91 REMARK 500 GLU A 123 81.41 68.91 REMARK 500 SER B 5 43.90 74.66 REMARK 500 GLU B 51 71.73 -166.12 REMARK 500 LEU B 70 -19.24 -48.04 REMARK 500 SER B 95 63.80 -101.08 REMARK 500 ASP B 120 -96.11 -101.95 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: REA REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: NULL REMARK 800 SITE_IDENTIFIER: REB REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: NULL DBREF 2GMF A 1 127 UNP P04141 CSF2_HUMAN 18 144 DBREF 2GMF B 1 127 UNP P04141 CSF2_HUMAN 18 144 SEQRES 1 A 127 ALA PRO ALA ARG SER PRO SER PRO SER THR GLN PRO TRP SEQRES 2 A 127 GLU HIS VAL ASN ALA ILE GLN GLU ALA ARG ARG LEU LEU SEQRES 3 A 127 ASN LEU SER ARG ASP THR ALA ALA GLU MET ASN GLU THR SEQRES 4 A 127 VAL GLU VAL ILE SER GLU MET PHE ASP LEU GLN GLU PRO SEQRES 5 A 127 THR CYS LEU GLN THR ARG LEU GLU LEU TYR LYS GLN GLY SEQRES 6 A 127 LEU ARG GLY SER LEU THR LYS LEU LYS GLY PRO LEU THR SEQRES 7 A 127 MET MET ALA SER HIS TYR LYS GLN HIS CYS PRO PRO THR SEQRES 8 A 127 PRO GLU THR SER CYS ALA THR GLN ILE ILE THR PHE GLU SEQRES 9 A 127 SER PHE LYS GLU ASN LEU LYS ASP PHE LEU LEU VAL ILE SEQRES 10 A 127 PRO PHE ASP CYS TRP GLU PRO VAL GLN GLU SEQRES 1 B 127 ALA PRO ALA ARG SER PRO SER PRO SER THR GLN PRO TRP SEQRES 2 B 127 GLU HIS VAL ASN ALA ILE GLN GLU ALA ARG ARG LEU LEU SEQRES 3 B 127 ASN LEU SER ARG ASP THR ALA ALA GLU MET ASN GLU THR SEQRES 4 B 127 VAL GLU VAL ILE SER GLU MET PHE ASP LEU GLN GLU PRO SEQRES 5 B 127 THR CYS LEU GLN THR ARG LEU GLU LEU TYR LYS GLN GLY SEQRES 6 B 127 LEU ARG GLY SER LEU THR LYS LEU LYS GLY PRO LEU THR SEQRES 7 B 127 MET MET ALA SER HIS TYR LYS GLN HIS CYS PRO PRO THR SEQRES 8 B 127 PRO GLU THR SER CYS ALA THR GLN ILE ILE THR PHE GLU SEQRES 9 B 127 SER PHE LYS GLU ASN LEU LYS ASP PHE LEU LEU VAL ILE SEQRES 10 B 127 PRO PHE ASP CYS TRP GLU PRO VAL GLN GLU FORMUL 3 HOH *92(H2 O) HELIX 1 AA TRP A 13 LEU A 28 1 16 HELIX 2 BA LEU A 55 GLN A 64 1 10 HELIX 3 CA LYS A 74 HIS A 87 1 14 HELIX 4 DA PHE A 103 VAL A 116 1 14 HELIX 5 EA GLY A 68 LEU A 73 5NON-CONSERVED FEATURE OF FOLD 6 HELIX 6 FA ALA A 33 MET A 36 1 4 HELIX 7 AB TRP B 13 LEU B 28 1 16 HELIX 8 BB LEU B 55 GLN B 64 1 10 HELIX 9 CB LYS B 74 HIS B 87 1 14 HELIX 10 DB PHE B 103 VAL B 116 1 14 HELIX 11 EB GLY B 68 LEU B 73 5NON-CONSERVED FEATURE OF FOLD 6 HELIX 12 FB ALA B 33 MET B 36 1 4 SHEET 1 S1 2 THR A 39 ILE A 43 0 SHEET 2 S1 2 THR A 98 THR A 102 -1 SHEET 1 S2 2 THR B 39 ILE B 43 0 SHEET 2 S2 2 THR B 98 THR B 102 -1 SSBOND 1 CYS A 54 CYS A 96 1555 1555 2.02 SSBOND 2 CYS A 88 CYS A 121 1555 1555 2.02 SSBOND 3 CYS B 54 CYS B 96 1555 1555 2.02 SSBOND 4 CYS B 88 CYS B 121 1555 1555 2.03 CISPEP 1 GLU A 123 PRO A 124 0 -0.23 SITE 1 REA 14 GLU A 14 ASN A 17 ALA A 18 GLU A 21 SITE 2 REA 14 ARG A 24 LEU A 25 LYS A 72 LYS A 74 SITE 3 REA 14 GLY A 75 PRO A 76 THR A 78 MET A 79 SITE 4 REA 14 SER A 82 GLN A 86 SITE 1 REB 14 GLU B 14 ASN B 17 ALA B 18 GLU B 21 SITE 2 REB 14 ARG B 24 LEU B 25 LYS B 72 LYS B 74 SITE 3 REB 14 GLY B 75 PRO B 76 THR B 78 MET B 79 SITE 4 REB 14 SER B 82 GLN B 86 CRYST1 47.520 59.060 126.290 90.00 90.00 90.00 P 21 21 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 0.021044 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016932 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007918 0.00000