PDB Short entry for 5LSD HEADER CELL CYCLE 25-AUG-16 5LSD TITLE RECOMBINANT MOUSE NERVE GROWTH FACTOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-NERVE GROWTH FACTOR; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: BETA-NGF; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: NGF IS A HOMODIMER SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: NGF, NGFB; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS NGF, HOMODIMER, CYSTIN-KNOT, DIMERFIT_1, CELL CYCLE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR F.PAOLETTI,C.DE CHIARA,G.KELLY,D.LAMBA,A.CATTANEO,A.PASTORE REVDAT 2 14-JUN-23 5LSD 1 JRNL REMARK REVDAT 1 05-JUL-17 5LSD 0 JRNL AUTH F.PAOLETTI,C.DE CHIARA,G.KELLY,S.COVACEUSZACH,F.MALERBA, JRNL AUTH 2 R.YAN,D.LAMBA,A.CATTANEO,A.PASTORE JRNL TITL CONFORMATIONAL RIGIDITY WITHIN PLASTICITY PROMOTES JRNL TITL 2 DIFFERENTIAL TARGET RECOGNITION OF NERVE GROWTH FACTOR. JRNL REF FRONT MOL BIOSCI V. 3 83 2016 JRNL REFN ESSN 2296-889X JRNL PMID 28083536 JRNL DOI 10.3389/FMOLB.2016.00083 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : ARIA 2.3.2 REMARK 3 AUTHORS : RIEPING W., HABECK M., BARDIAUX B., BERNARD A., REMARK 3 MALLIAVIN T.E., NILGES M. (2007) ARIA2: AUTOMATED REMARK 3 NOE ASSIGNMENT AND DATA INTEGRATION IN NMR REMARK 3 STRUCTURE CALCULATION BIOINFORMATICS 23:381-382 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5LSD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 25-AUG-16. REMARK 100 THE DEPOSITION ID IS D_1200001248. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303; 308 REMARK 210 PH : 7; 7 REMARK 210 IONIC STRENGTH : 50; 50 REMARK 210 PRESSURE : 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 0.1 MM [U-99% 13C; U-99% 15N] REMARK 210 NERVE GROWTH FACTOR, 50 MM REMARK 210 SODIUM PHOSPHATE, 1 MM EDTA, 93% REMARK 210 H2O/7% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D HNCA; 2D 1H-15N HSQC; 3D REMARK 210 HNCO; 3D HNCACB; 3D 1H-15N NOESY; REMARK 210 2D 1H-13C HSQC ALIPHATIC; 3D 1H- REMARK 210 13C NOESY ALIPHATIC; 3D CBCA(CO) REMARK 210 NH; 3D HCCH-TOCSY; 2D 1H-13C REMARK 210 HSQC AROMATIC; 3D 1H-13C NOESY REMARK 210 AROMATIC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ; 700 MHZ REMARK 210 SPECTROMETER MODEL : INOVA; AVANCE REMARK 210 SPECTROMETER MANUFACTURER : VARIAN; BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE, NMRDRAW, CARA, ARIA REMARK 210 2.3.2 REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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: 3300 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13990 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.0 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE 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 1 THR A 3 44.49 -84.35 REMARK 500 1 PRO A 5 41.34 -83.24 REMARK 500 1 PHE A 7 -69.62 65.44 REMARK 500 1 HIS A 8 51.23 -148.87 REMARK 500 1 GLU A 11 -43.80 71.91 REMARK 500 1 ILE A 44 -81.09 -82.64 REMARK 500 1 ASN A 45 -68.09 -124.81 REMARK 500 1 TYR A 52 161.12 64.01 REMARK 500 1 SER A 66 -33.29 -179.50 REMARK 500 1 ASP A 72 95.09 -68.74 REMARK 500 1 GLU A 94 -73.00 -166.11 REMARK 500 1 THR B 3 44.23 -83.19 REMARK 500 1 PRO B 5 41.37 -83.05 REMARK 500 1 PHE B 7 -69.67 65.51 REMARK 500 1 HIS B 8 51.18 -148.94 REMARK 500 1 GLU B 11 -44.00 71.91 REMARK 500 1 ILE B 44 -81.08 -82.69 REMARK 500 1 ASN B 45 -68.60 -124.68 REMARK 500 1 TYR B 52 161.27 63.81 REMARK 500 1 SER B 66 -33.21 -179.69 REMARK 500 1 ASP B 72 95.29 -68.64 REMARK 500 1 GLU B 94 -73.31 -165.75 REMARK 500 2 SER A 2 -72.83 -138.02 REMARK 500 2 PRO A 5 94.40 -64.62 REMARK 500 2 PHE A 7 -70.66 68.31 REMARK 500 2 HIS A 8 56.83 -154.67 REMARK 500 2 MET A 9 -48.95 74.04 REMARK 500 2 ILE A 44 132.78 70.42 REMARK 500 2 ASN A 46 -54.60 -167.33 REMARK 500 2 SER A 61 39.08 -158.49 REMARK 500 2 PRO A 63 -64.16 -21.99 REMARK 500 2 VAL A 64 -92.75 -95.91 REMARK 500 2 ARG A 69 151.19 67.81 REMARK 500 2 GLU A 94 -40.71 -169.52 REMARK 500 2 LYS A 95 -67.37 -131.85 REMARK 500 2 ALA A 116 -56.59 -126.54 REMARK 500 2 SER B 2 -73.36 -138.04 REMARK 500 2 PRO B 5 94.37 -64.92 REMARK 500 2 PHE B 7 -70.74 67.89 REMARK 500 2 HIS B 8 57.05 -154.52 REMARK 500 2 MET B 9 -48.79 73.79 REMARK 500 2 ILE B 44 132.81 70.47 REMARK 500 2 ASN B 46 -55.13 -166.72 REMARK 500 2 SER B 61 38.48 -158.32 REMARK 500 2 PRO B 63 -64.47 -21.85 REMARK 500 2 VAL B 64 -92.87 -95.46 REMARK 500 2 ARG B 69 151.16 67.77 REMARK 500 2 GLU B 94 -40.22 -169.78 REMARK 500 2 LYS B 95 -67.93 -132.17 REMARK 500 2 ALA B 116 -56.34 -127.18 REMARK 500 REMARK 500 THIS ENTRY HAS 373 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34037 RELATED DB: BMRB REMARK 900 RECOMBINANT MOUSE NERVE GROWTH FACTOR DBREF 5LSD A 1 118 UNP P01139 NGF_MOUSE 122 239 DBREF 5LSD B 1 118 UNP P01139 NGF_MOUSE 122 239 SEQRES 1 A 118 SER SER THR HIS PRO VAL PHE HIS MET GLY GLU PHE SER SEQRES 2 A 118 VAL CYS ASP SER VAL SER VAL TRP VAL GLY ASP LYS THR SEQRES 3 A 118 THR ALA THR ASP ILE LYS GLY LYS GLU VAL THR VAL LEU SEQRES 4 A 118 ALA GLU VAL ASN ILE ASN ASN SER VAL PHE ARG GLN TYR SEQRES 5 A 118 PHE PHE GLU THR LYS CYS ARG ALA SER ASN PRO VAL GLU SEQRES 6 A 118 SER GLY CYS ARG GLY ILE ASP SER LYS HIS TRP ASN SER SEQRES 7 A 118 TYR CYS THR THR THR HIS THR PHE VAL LYS ALA LEU THR SEQRES 8 A 118 THR ASP GLU LYS GLN ALA ALA TRP ARG PHE ILE ARG ILE SEQRES 9 A 118 ASP THR ALA CYS VAL CYS VAL LEU SER ARG LYS ALA THR SEQRES 10 A 118 ARG SEQRES 1 B 118 SER SER THR HIS PRO VAL PHE HIS MET GLY GLU PHE SER SEQRES 2 B 118 VAL CYS ASP SER VAL SER VAL TRP VAL GLY ASP LYS THR SEQRES 3 B 118 THR ALA THR ASP ILE LYS GLY LYS GLU VAL THR VAL LEU SEQRES 4 B 118 ALA GLU VAL ASN ILE ASN ASN SER VAL PHE ARG GLN TYR SEQRES 5 B 118 PHE PHE GLU THR LYS CYS ARG ALA SER ASN PRO VAL GLU SEQRES 6 B 118 SER GLY CYS ARG GLY ILE ASP SER LYS HIS TRP ASN SER SEQRES 7 B 118 TYR CYS THR THR THR HIS THR PHE VAL LYS ALA LEU THR SEQRES 8 B 118 THR ASP GLU LYS GLN ALA ALA TRP ARG PHE ILE ARG ILE SEQRES 9 B 118 ASP THR ALA CYS VAL CYS VAL LEU SER ARG LYS ALA THR SEQRES 10 B 118 ARG HELIX 1 AA1 PRO A 5 GLY A 10 1 6 HELIX 2 AA2 PRO B 5 GLY B 10 1 6 SHEET 1 AA1 2 SER A 17 VAL A 22 0 SHEET 2 AA1 2 PHE A 53 CYS A 58 -1 O GLU A 55 N VAL A 20 SHEET 1 AA2 4 THR A 27 THR A 29 0 SHEET 2 AA2 4 GLU A 35 VAL A 38 -1 O VAL A 36 N ALA A 28 SHEET 3 AA2 4 ASN A 77 THR A 92 -1 O THR A 92 N THR A 37 SHEET 4 AA2 4 ALA A 97 SER A 113 -1 O ALA A 98 N THR A 91 SHEET 1 AA3 2 GLU A 41 ASN A 43 0 SHEET 2 AA3 2 VAL A 48 ARG A 50 -1 O PHE A 49 N VAL A 42 SHEET 1 AA4 2 SER B 17 VAL B 22 0 SHEET 2 AA4 2 PHE B 53 CYS B 58 -1 O GLU B 55 N VAL B 20 SHEET 1 AA5 4 THR B 27 THR B 29 0 SHEET 2 AA5 4 GLU B 35 VAL B 38 -1 O VAL B 36 N ALA B 28 SHEET 3 AA5 4 ASN B 77 THR B 92 -1 O THR B 92 N THR B 37 SHEET 4 AA5 4 ALA B 97 SER B 113 -1 O VAL B 109 N THR B 81 SHEET 1 AA6 2 GLU B 41 ASN B 43 0 SHEET 2 AA6 2 VAL B 48 ARG B 50 -1 O PHE B 49 N VAL B 42 SSBOND 1 CYS A 15 CYS A 80 1555 1555 2.03 SSBOND 2 CYS A 58 CYS A 108 1555 1555 2.03 SSBOND 3 CYS A 68 CYS A 110 1555 1555 2.03 SSBOND 4 CYS B 15 CYS B 80 1555 1555 2.03 SSBOND 5 CYS B 58 CYS B 108 1555 1555 2.03 SSBOND 6 CYS B 68 CYS B 110 1555 1555 2.03 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000