HEADER LIPID BINDING PROTEIN 14-OCT-21 7Q02 TITLE ZN-FREE STRUCTURE OF LIPOCALIN-LIKE MILK PROTEIN, INSPIRED FROM TITLE 2 DIPLOPTERA PUNCTATA, EXPRESSED IN SACCHAROMYCES CEREVISIAE COMPND MOL_ID: 1; COMPND 2 MOLECULE: MILK PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DIPLOPTERA PUNCTATA; SOURCE 3 ORGANISM_COMMON: PACIFIC BEETLE COCKROACH; SOURCE 4 ORGANISM_TAXID: 6984; SOURCE 5 EXPRESSION_SYSTEM: SACCHAROMYCES CEREVISIAE; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 4932 KEYWDS LIPOCALIN, MILK PROTEIN, DIPOLPTERA PUNCTATA, LIPID BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.BANERJEE,K.V.DHANABALAN,S.RAMASWAMY REVDAT 3 31-JAN-24 7Q02 1 REMARK REVDAT 2 18-MAY-22 7Q02 1 JRNL REVDAT 1 22-DEC-21 7Q02 0 JRNL AUTH D.KANAGAVIJAYAN,R.SUBRAMANIAN,P.R.SANTHAKUMARI,L.M.G.CHAVAS, JRNL AUTH 2 S.BANERJEE JRNL TITL STRUCTURE OF RECOMBINANTLY EXPRESSED COCKROACH LILI-MIP JRNL TITL 2 PROTEIN IN GLYCOSYLATED AND DEGLYCOSYLATED FORMS. JRNL REF BIOCHIM BIOPHYS ACTA GEN V.1866 30064 2022 JRNL REF 2 SUBJ JRNL REFN ISSN 1872-8006 JRNL PMID 34958847 JRNL DOI 10.1016/J.BBAGEN.2021.130064 REMARK 2 REMARK 2 RESOLUTION. 1.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19_4092 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.81 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 28372 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.152 REMARK 3 R VALUE (WORKING SET) : 0.150 REMARK 3 FREE R VALUE : 0.195 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.940 REMARK 3 FREE R VALUE TEST SET COUNT : 1402 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 48.8100 - 3.1200 1.00 2884 147 0.1414 0.1762 REMARK 3 2 3.1200 - 2.4800 1.00 2769 126 0.1561 0.1938 REMARK 3 3 2.4800 - 2.1700 1.00 2718 121 0.1437 0.1886 REMARK 3 4 2.1700 - 1.9700 1.00 2686 142 0.1348 0.2017 REMARK 3 5 1.9700 - 1.8300 1.00 2673 152 0.1418 0.1733 REMARK 3 6 1.8300 - 1.7200 1.00 2647 154 0.1595 0.2136 REMARK 3 7 1.7200 - 1.6300 1.00 2683 130 0.1565 0.1923 REMARK 3 8 1.6300 - 1.5600 1.00 2656 136 0.1603 0.2220 REMARK 3 9 1.5600 - 1.5000 1.00 2653 141 0.1700 0.2229 REMARK 3 10 1.5000 - 1.4500 1.00 2601 153 0.2192 0.2868 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.130 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.320 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.79 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.44 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7Q02 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 19-OCT-21. REMARK 100 THE DEPOSITION ID IS D_1292118705. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-OCT-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 23-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0332 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.7 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28438 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.450 REMARK 200 RESOLUTION RANGE LOW (A) : 48.810 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : 0.10700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.48 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.50 REMARK 200 R MERGE FOR SHELL (I) : 0.77100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 4NYQ REMARK 200 REMARK 200 REMARK: PLATE-LIKE CRYSTALS. REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.26 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM ACETATE, HCL, PH 4.5; 25 REMARK 280 % (W/V) PEG 3350, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 290K 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 16.68100 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 48.80600 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.84600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 48.80600 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.68100 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 23.84600 REMARK 290 SMTRY3 4 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 770 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7770 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 1.0 KCAL/MOL 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 ILE A -8 REMARK 465 ALA A -7 REMARK 465 ALA A -6 REMARK 465 ILE A -5 REMARK 465 LEU A -4 REMARK 465 VAL A -3 REMARK 465 ALA A -2 REMARK 465 ASN A -1 REMARK 465 ALA A 0 REMARK 465 LEU A 154 REMARK 465 GLU A 155 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 LYS A 127 CD CE NZ REMARK 470 LYS A 131 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 ALA A 107 69.84 -151.53 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7BKX RELATED DB: PDB DBREF 7Q02 A -8 155 UNP Q6SVB5 Q6SVB5_DIPPU 1 164 SEQRES 1 A 164 ILE ALA ALA ILE LEU VAL ALA ASN ALA LYS GLU PRO CYS SEQRES 2 A 164 PRO PRO GLU ASN LEU GLN LEU THR PRO ARG ALA LEU VAL SEQRES 3 A 164 GLY LYS TRP TYR LEU ARG THR THR SER PRO ASP ILE PHE SEQRES 4 A 164 LYS GLN VAL SER ASN ILE THR GLU PHE TYR SER ALA HIS SEQRES 5 A 164 GLY ASN ASP TYR TYR GLY THR VAL THR ASP TYR SER PRO SEQRES 6 A 164 GLU TYR GLY LEU GLU ALA HIS ARG VAL ASN LEU THR VAL SEQRES 7 A 164 SER GLY ARG THR LEU LYS PHE TYR MET ASN ASP THR HIS SEQRES 8 A 164 GLU TYR ASP SER GLU TYR GLU ILE LEU ALA VAL ASP LYS SEQRES 9 A 164 ASP TYR PHE ILE PHE TYR GLY HIS PRO PRO ALA ALA PRO SEQRES 10 A 164 SER GLY LEU ALA LEU ILE HIS TYR ARG GLN SER CYS PRO SEQRES 11 A 164 LYS GLU ASP ILE ILE LYS ARG VAL LYS LYS SER LEU LYS SEQRES 12 A 164 ASN VAL CYS LEU ASP TYR LYS TYR PHE GLY ASN ASP THR SEQRES 13 A 164 SER VAL HIS CYS ARG TYR LEU GLU HET PAM A 201 18 HETNAM PAM PALMITOLEIC ACID FORMUL 2 PAM C16 H30 O2 FORMUL 3 HOH *224(H2 O) HELIX 1 AA1 LYS A 122 VAL A 136 1 15 HELIX 2 AA2 ASP A 139 PHE A 143 5 5 SHEET 1 AA110 GLY A 144 ASN A 145 0 SHEET 2 AA110 GLY A 18 SER A 26 -1 N THR A 25 O GLY A 144 SHEET 3 AA110 LEU A 111 TYR A 116 -1 O TYR A 116 N TYR A 21 SHEET 4 AA110 TYR A 97 GLY A 102 -1 N PHE A 98 O HIS A 115 SHEET 5 AA110 SER A 86 ASP A 94 -1 N LEU A 91 O ILE A 99 SHEET 6 AA110 THR A 73 MET A 78 -1 N LEU A 74 O TYR A 88 SHEET 7 AA110 GLY A 59 SER A 70 -1 N SER A 70 O THR A 73 SHEET 8 AA110 ASP A 46 SER A 55 -1 N VAL A 51 O HIS A 63 SHEET 9 AA110 SER A 34 HIS A 43 -1 N SER A 34 O TYR A 54 SHEET 10 AA110 GLY A 18 SER A 26 -1 N TRP A 20 O GLU A 38 SSBOND 1 CYS A 4 CYS A 137 1555 1555 2.06 SSBOND 2 CYS A 120 CYS A 151 1555 1555 2.05 CISPEP 1 SER A 26 PRO A 27 0 -2.56 CRYST1 33.362 47.692 97.612 90.00 90.00 90.00 P 21 21 21 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 0.029974 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020968 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010245 0.00000