PDB Short entry for 2KPW HEADER STRUCTURAL PROTEIN 21-OCT-09 2KPW TITLE NMR SOLUTION STRUCTURE OF LAMIN-B1 PROTEIN FROM HOMO SAPIENS: TITLE 2 NORTHEAST STRUCTURAL GENOMICS CONSORTIUM MEGA TARGET, HR5546A (439- TITLE 3 549) COMPND MOL_ID: 1; COMPND 2 MOLECULE: LAMIN-B1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SEQUENCE DATABASE RESIDUES 439-549; 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: LMN2, LMNB, LMNB1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)+MAGIC; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PET 14-15C KEYWDS PSI-2, NESG, HR5546A, LAMIN-B1, GFT, ACETYLATION, CHROMOSOMAL KEYWDS 2 REARRANGEMENT, COILED COIL, INTERMEDIATE FILAMENT, LEUKODYSTROPHY, KEYWDS 3 LIPOPROTEIN, MEMBRANE, NUCLEUS, PHOSPHOPROTEIN, POLYMORPHISM, KEYWDS 4 PRENYLATION, STRUCTURAL GENOMICS, PROTEIN STRUCTURE INITIATIVE, KEYWDS 5 NORTHEAST STRUCTURAL GENOMICS CONSORTIUM, STRUCTURAL PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR G.V.T.SWAPNA,C.L.CICCOSANTI,R.BELOTE,K.HAMILTON,T.ACTON,Y.HUANG, AUTHOR 2 R.XIAO,J.EVERETT,G.T.MONTELIONE,NORTHEAST STRUCTURAL GENOMICS AUTHOR 3 CONSORTIUM (NESG) REVDAT 5 14-JUN-23 2KPW 1 REMARK REVDAT 4 18-AUG-21 2KPW 1 REMARK REVDAT 3 26-FEB-20 2KPW 1 REMARK SEQADV REVDAT 2 24-NOV-09 2KPW 1 KEYWDS REVDAT 1 10-NOV-09 2KPW 0 JRNL AUTH G.V.T.SWAPNA,C.CICCOSANTI,R.L.BELOTE,K.HAMILTON,T.ACTON, JRNL AUTH 2 Y.HUANG,R.XIAO,J.EVERETT,G.T.MONTELIONE JRNL TITL NMR SOLUTION STRUCTURE OF LAMIN-B1 PROTEIN FROM HOMO JRNL TITL 2 SAPIENS: NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET, JRNL TITL 3 HR5546A (439-549) JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 2.0.6 REMARK 3 AUTHORS : BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: FINAL STRUCTURE QUALITY FACTORS REMARK 3 DETERMINED USING PSVS SOFTWARE: ORDERED RESIDUES ARE DEFINED AS: REMARK 3 15A-32A,34A-37A,42A-47A,53A-72A,75A-79A,85A-91A,101A-106A, 110A- REMARK 3 116A.(A) RMSD(ORDERED RESIDUES):BACKBONE ATOMS: 0.7A; ALL ATOMS: REMARK 3 1.0A.(B) RAMACHANDRAN STATISTICS FOR ALL ORDERED RESIDUES: MOST REMARK 3 FAVOURED REGIONS: 83.1% ADDITIONALLY ALLOWED REGIONS:16.9% (C) REMARK 3 PROCHECK SCORES FOR ALL ORDERED RESIDUES (RAW/Z): PHI-PSI -0.76/- REMARK 3 2.68, ALL: -0.42/-2.48 (D) MOLPROBITY CLASH SCORE (RAW/Z): 20.38/ REMARK 3 -1.97. (E) RPF SCORES FOR GOODNESS OF FIT TO NOESY DATA: RECALL: REMARK 3 0.962 PRECISION: 0.919 F-MEASURE: 0.94 DP-SCORE 0.794. REMARK 4 REMARK 4 2KPW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-OCT-09. REMARK 100 THE DEPOSITION ID IS D_1000101425. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 4.5 REMARK 210 IONIC STRENGTH : 20MM NH4OAC, 5MM CACL2, 200MM REMARK 210 NACL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.129 MM [U-100% 13C; U-100% REMARK 210 15N] LAMIN-B1 PROTEIN, 90% H2O/ REMARK 210 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D HNCACB; 3D CBCA(CO)NH; 3D REMARK 210 HBHA(CO)NH; 3D HNCO; 3D HNHA; 3D REMARK 210 HCCH-TOCSY; 3D 1H-15N NOESY; 3D REMARK 210 1H-13C NOESY; 2D HNOE REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : INOVA; AVANCE REMARK 210 SPECTROMETER MANUFACTURER : VARIAN; BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : AUTOASSIGN 2.1, AVS, NMRPIPE REMARK 210 2008, SPARKY 2.3, AUTOSTRUCTURE REMARK 210 2.2.1, CYANA 2.1, TOPSPIN 2.1, REMARK 210 VNMRJ 2.1 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 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: THE STRUCTURE WAS DETERMINED USING TRIPLE RESONANCE REMARK 210 SPECTROSCOPY. DATA FOR THE BACKBONE ASSIGNMENTS WAS ACQUIRED REMARK 210 USING GFT NMR EXPERIMENTS. AUTOMATED RESONANCE ASSIGNMENTS WERE REMARK 210 MADE USING AUTOASSIGN AND PATTERN-PICKER ALGORITHMS DEVELOPED REMARK 210 FOR AUTOMATED ASSIGNMENTS OF GFT DATA. SIDE CHAIN ASSIGNMENTS REMARK 210 WERE COMPLETED MANUALLY. AUTOMATED NOESY ASSIGNMENTS WERE MADE REMARK 210 USING AUTOSTRUCTURE AND STRUCTURE SOLUTION WAS DETERMINED USING REMARK 210 CYANA-2.1. 100 STRUCTURES WERE CALCULATED AND 20 BEST CONFORMERS REMARK 210 WERE THEN REFINED IN A SHELL OF WATER USING CNS. INITIAL REMARK 210 DIHEDRAL ANGLE CONSTRIANTS WERE OBTAINED FROM TALOS. REMARK 210 COMPLETENESS OF THE ASSIGNMENTS INCLUDING THE N-TERMINAL 6XHIS REMARK 210 TAG WERE BACKBONE:99% SIDECHAIN: 96%. THE ASSIGNMENTS WERE REMARK 210 VALIDATED USING AVS SOFTWARE. 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: 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 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 HIS A 4 148.50 -171.11 REMARK 500 1 HIS A 7 116.88 -166.43 REMARK 500 1 THR A 32 40.84 -109.36 REMARK 500 1 ILE A 48 -53.80 -164.51 REMARK 500 1 ASP A 50 -69.24 69.07 REMARK 500 1 ALA A 74 -73.37 60.66 REMARK 500 1 ALA A 76 -39.94 -133.03 REMARK 500 1 SER A 81 71.45 67.25 REMARK 500 1 PRO A 83 60.79 13.41 REMARK 500 1 THR A 84 -52.93 153.68 REMARK 500 1 TRP A 88 91.04 -69.14 REMARK 500 1 THR A 96 28.34 -79.83 REMARK 500 1 ASP A 99 101.63 -52.63 REMARK 500 1 PHE A 119 91.65 -64.19 REMARK 500 2 HIS A 8 90.68 -57.52 REMARK 500 2 SER A 9 -169.68 -126.72 REMARK 500 2 ASN A 14 81.00 -68.16 REMARK 500 2 ILE A 48 21.48 -150.22 REMARK 500 2 SER A 52 33.03 -145.37 REMARK 500 2 ASN A 75 43.18 -93.71 REMARK 500 2 ASP A 99 89.18 -67.92 REMARK 500 3 SER A 81 81.36 59.83 REMARK 500 3 THR A 84 -38.20 -171.02 REMARK 500 3 THR A 96 -27.27 176.46 REMARK 500 3 ASP A 99 99.32 -64.52 REMARK 500 3 ALA A 113 133.70 -176.67 REMARK 500 4 ASN A 14 47.69 -76.84 REMARK 500 4 GLU A 18 -69.25 -90.56 REMARK 500 4 LYS A 30 119.90 -162.66 REMARK 500 4 ILE A 48 -41.43 -135.99 REMARK 500 4 ASP A 50 -36.51 72.47 REMARK 500 4 THR A 84 -56.36 -154.96 REMARK 500 4 THR A 96 26.25 -157.35 REMARK 500 5 THR A 12 32.19 -91.38 REMARK 500 5 PRO A 38 29.90 -74.80 REMARK 500 5 MET A 39 -71.18 64.94 REMARK 500 5 ASP A 50 -58.75 76.46 REMARK 500 5 PRO A 82 170.84 -48.79 REMARK 500 5 PRO A 83 -80.51 -16.82 REMARK 500 5 THR A 84 -83.63 -78.62 REMARK 500 5 TRP A 88 77.90 -69.46 REMARK 500 5 LYS A 89 27.82 -75.88 REMARK 500 6 HIS A 3 39.70 -144.66 REMARK 500 6 HIS A 7 99.43 -66.00 REMARK 500 6 MET A 11 108.88 61.58 REMARK 500 6 THR A 12 36.51 -94.26 REMARK 500 6 MET A 39 -72.26 -52.45 REMARK 500 6 TYR A 55 114.21 -160.47 REMARK 500 6 SER A 59 33.93 -85.89 REMARK 500 6 VAL A 69 106.66 -57.96 REMARK 500 REMARK 500 THIS ENTRY HAS 197 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 PRO A 82 PRO A 83 1 38.83 REMARK 500 PRO A 82 PRO A 83 7 36.16 REMARK 500 PRO A 82 PRO A 83 9 38.02 REMARK 500 PRO A 82 PRO A 83 17 44.60 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 16572 RELATED DB: BMRB REMARK 900 RELATED ID: HR5546A RELATED DB: TARGETDB DBREF 2KPW A 12 122 UNP P20700 LMNB1_HUMAN 439 549 SEQADV 2KPW MET A 1 UNP P20700 EXPRESSION TAG SEQADV 2KPW GLY A 2 UNP P20700 EXPRESSION TAG SEQADV 2KPW HIS A 3 UNP P20700 EXPRESSION TAG SEQADV 2KPW HIS A 4 UNP P20700 EXPRESSION TAG SEQADV 2KPW HIS A 5 UNP P20700 EXPRESSION TAG SEQADV 2KPW HIS A 6 UNP P20700 EXPRESSION TAG SEQADV 2KPW HIS A 7 UNP P20700 EXPRESSION TAG SEQADV 2KPW HIS A 8 UNP P20700 EXPRESSION TAG SEQADV 2KPW SER A 9 UNP P20700 EXPRESSION TAG SEQADV 2KPW HIS A 10 UNP P20700 EXPRESSION TAG SEQADV 2KPW MET A 11 UNP P20700 EXPRESSION TAG SEQRES 1 A 122 MET GLY HIS HIS HIS HIS HIS HIS SER HIS MET THR GLY SEQRES 2 A 122 ASN VAL CYS ILE GLU GLU ILE ASP VAL ASP GLY LYS PHE SEQRES 3 A 122 ILE ARG LEU LYS ASN THR SER GLU GLN ASP GLN PRO MET SEQRES 4 A 122 GLY GLY TRP GLU MET ILE ARG LYS ILE GLY ASP THR SER SEQRES 5 A 122 VAL SER TYR LYS TYR THR SER ARG TYR VAL LEU LYS ALA SEQRES 6 A 122 GLY GLN THR VAL THR ILE TRP ALA ALA ASN ALA GLY VAL SEQRES 7 A 122 THR ALA SER PRO PRO THR ASP LEU ILE TRP LYS ASN GLN SEQRES 8 A 122 ASN SER TRP GLY THR GLY GLU ASP VAL LYS VAL ILE LEU SEQRES 9 A 122 LYS ASN SER GLN GLY GLU GLU VAL ALA GLN ARG SER THR SEQRES 10 A 122 VAL PHE LYS THR THR SHEET 1 A 4 VAL A 15 ILE A 20 0 SHEET 2 A 4 PHE A 26 ASN A 31 -1 O LYS A 30 N CYS A 16 SHEET 3 A 4 GLN A 67 TRP A 72 -1 O ILE A 71 N ILE A 27 SHEET 4 A 4 LEU A 86 ILE A 87 1 O LEU A 86 N THR A 70 SHEET 1 B 2 GLN A 37 PRO A 38 0 SHEET 2 B 2 VAL A 62 LEU A 63 -1 O LEU A 63 N GLN A 37 SHEET 1 C 4 SER A 52 LYS A 56 0 SHEET 2 C 4 GLU A 43 LYS A 47 -1 N MET A 44 O TYR A 55 SHEET 3 C 4 LYS A 101 LYS A 105 -1 O LYS A 101 N LYS A 47 SHEET 4 C 4 GLU A 111 SER A 116 -1 O ARG A 115 N VAL A 102 CISPEP 1 PRO A 82 PRO A 83 2 -0.92 CISPEP 2 PRO A 82 PRO A 83 3 -1.74 CISPEP 3 PRO A 82 PRO A 83 4 -0.52 CISPEP 4 PRO A 82 PRO A 83 5 11.18 CISPEP 5 PRO A 82 PRO A 83 6 6.27 CISPEP 6 PRO A 82 PRO A 83 8 17.11 CISPEP 7 PRO A 82 PRO A 83 10 3.06 CISPEP 8 PRO A 82 PRO A 83 11 5.27 CISPEP 9 PRO A 82 PRO A 83 12 -1.15 CISPEP 10 PRO A 82 PRO A 83 13 6.39 CISPEP 11 PRO A 82 PRO A 83 14 -1.62 CISPEP 12 PRO A 82 PRO A 83 15 25.21 CISPEP 13 PRO A 82 PRO A 83 16 1.44 CISPEP 14 PRO A 82 PRO A 83 18 2.10 CISPEP 15 PRO A 82 PRO A 83 19 11.03 CISPEP 16 PRO A 82 PRO A 83 20 -2.98 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